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. 2017 May;31(3):928-939.
doi: 10.1111/jvim.14695. Epub 2017 Apr 7.

Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves

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Characterization of the Fecal Bacterial Microbiota of Healthy and Diarrheic Dairy Calves

D E Gomez et al. J Vet Intern Med. 2017 May.

Abstract

Background: Neonatal diarrhea accounts for more than 50% of total deaths in dairy calves. Few population-based studies of cattle have investigated how the microbiota is impacted during diarrhea.

Objectives: To characterize the fecal microbiota and predict the functional potential of the microbial communities in healthy and diarrheic calves.

Methods: Fifteen diarrheic calves between the ages of 1 and 30 days and 15 age-matched healthy control calves were enrolled from 2 dairy farms. The Illumina MiSeq sequencer was used for high-throughput sequencing of the V4 region of the 16S rRNA gene (Illumina, San Diego, CA).

Results: Significant differences in community membership and structure were identified among healthy calves from different farms. Differences in community membership and structure also were identified between healthy and diarrheic calves within each farm. Based on linear discriminant analysis effect size (LEfSe), the genera Bifidobacterium, Megamonas, and a genus of the family Bifidobacteriaceae were associated with health at farm 1, whereas Lachnospiraceae incertae sedis, Dietzia and an unclassified genus of the family Veillonellaceae were significantly associated with health at farm 2. The Phylogenetic Investigation of Communities Reconstruction of Unobserved States (PICRUSt) analysis indicated that diarrheic calves had decreased abundances of genes responsible for metabolism of various vitamins, amino acids, and carbohydrate.

Clinical relevance: The fecal microbiota of healthy dairy calves appeared to be farm specific as were the changes observed during diarrhea. The differences in microbiota structure and membership between healthy and diarrheic calves suggest that dysbiosis can occur in diarrheic calves and it is associated with changes in predictive metagenomic function.

Keywords: Escherichia coli; Bacterial species; Bifidobacterium; Epidemiology; Infectious diseases; LEfSe; Microbiology; PICRUSt.

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Figures

Figure 1
Figure 1
Richness (Chao‐1), diversity (Inverse Simpson), and evenness (Shannon evenness) indexes observed in healthy and diarrheic calves from 2 different farms.
Figure 2
Figure 2
Median relative abundance of the main bacterial phyla (>1% of the total of sequences) in feces of healthy and diarrheic calves from 2 different farms (n = 15 per group).
Figure 3
Figure 3
Median relative abundance of genera accounting for >1% of the total of sequences in feces of healthy and diarrheic calves from 2 different farms (n = 15 per group).
Figure 4
Figure 4
Cladogram plotted from LEfSe analysis showing the taxonomic levels represented by rings with phyla in the outermost the ring and genera in the innermost ring. Each circle is a member within that level. Those taxa in each level are coloured by farm for which it is more abundant (P < .05; LDA score 2).
Figure 5
Figure 5
Plot from LEfSe analysis indicating enriched bacterial genera associated either with healthy (green) or diarrheic (red) calves from farm 1.
Figure 6
Figure 6
Plot from LEfSe analysis indicating enriched genera associated either with healthy (green) or diarrheic (red) calves from farm 2. *Editorial office note: Figure is clear when downloaded and viewed on computer. Figure is blurry when compiled into a PDF of full article. If this manuscript is published, the publishers’ production team will make sure figure is represented clearly in final representation.
Figure 7
Figure 7
Dendrograms representing the similarity of community membership (Jaccard index, left panel) and structure (Yue and Clayton index, right panel) found in fecal samples collected from healthy (blue) and diarrheic (red) calves from farm 1 and healthy (green) and diarrheic (yellow) calves from farm 2.
Figure 8
Figure 8
Three‐dimensional principal coordinates analyses of the community membership (Jaccard Index) of the fecal microbiota of healthy and diarrheic calves. Coloured points and ellipses indicate groups: healthy calves from farm 1 (green) and farm 2 (red) and diarrheic calves from farm 1 (orange) and farm 2 (blue).
Figure 9
Figure 9
Three‐dimensional principal coordinates analyses of the community structure (Yue and Clayton index) of the fecal microbiota of healthy and diarrheic calves. Coloured points and ellipses indicate groups: healthy calves from farm 1 (green) and farm 2 (red) and diarrheic calves from farm 1 (orange) and farm 2 (blue).
Figure 10
Figure 10
Predicted functional composition of metagenomes based on 16S rRNA gene sequencing data. LEfSe based on the PICRUSt dataset revealed differentially enriched metabolic pathways associated either with healthy (green) or diarrheic calves (red) from farm 2.

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