Network analysis and functional estimation of the microbiome reveal the effects of cashew nut shell liquid feeding on methanogen behaviour in the rumen

Figures

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  Fig. 1. Enteric CH4 (dark grey) and CO2 (light grey) emissions per kg dry matter intake (DMI) from Lai Sind cattle with (periods 2–4) and without (period 1) CNSL feeding (n = 4). Error bars: standard deviation (SD). Different letters indicate significant differences (P < 0.05). Different doses of CNSL were set in Run 1 (4 g/100 kg BW) and Run 2 (6 g/100 kg BW).

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  Fig. 2. Changes in the δ13C values of enteric CH4 (Run 1). The δ13C values are expressed as relative to the VPDB (Vienna Pee Dee Belemnite). Each symbol (circle, triangle, square and diamond) indicates individual cattle. Error bar: SD (n = 3).

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  Fig. 3. Changes in the ruminal microbiome over time. The ruminal total bacterial/archaeal composition is shown with the order level (A) and family/genus level (B) by the amplicon sequencing of partial 16S rRNA gene. ‘Period’ and ‘CNSL’ indicate the sampling period (after CNSL feeding; period 1 indicates just before CNSL feeding) of ruminal fluid with (+) or without (−) CNSL feeding. (C) Principal component analysis of the ruminal microbiome over time. Each colour indicates a different individual. Circle: period 1, triangle: period 2, square: period 3, diamond: period 4. (D, E) Network analysis of the rumen microbiome in periods 1 (D) and 4 (E). Data from both runs were analysed together. The relative abundance of each group is reflected in the size of the circles. Colours of the lines between each circle indicate the correlation coefficient, from low (red) to high (blue) correlation. Only significant correlations (r > 0.5) are shown.

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  Fig. 4. Predicted functions of the ruminal microbiome by PICRUSt. A. The effect of CNSL feeding on ruminal functions related to feed digestion. Only higher hierarchies in KEGG pathways were selected. B. Significantly changed features by CNSL feeding in Run 1. Orange and light blue at the bottom of the dendrogram indicate the results with (periods 2–4) and without (period 1) CNSL feeding. C. Significantly changed features by CNSL feeding in Run 2. The lower hierarchy in KEGG pathways that was related to feed digestion and nutrient intake was selected.