Analysis of the Rumen Microbiome and Metabolome to Study the Effect of an Antimethanogenic Treatment Applied in Early Life of Kid Goats

Abstract

This work aimed to gain insight into the transition from milk to solid feeding at weaning combining genomics and metabolomics on rumen contents from goat kids treated with a methanogenic inhibitor (bromochloromethane, BCM). Sixteen goats giving birth to two kids were used. Eight does were treated (D+) with BCM after giving birth and over 2 months. One kid per doe in both groups was treated with BCM (k+) for 3 months while the other was untreated (k-). Rumen samples were collected from kids at weaning (W) and 1 (W + 1) and 4 (W + 4) months after and from does at weaning and subjected to 16S pyrosequencing and metabolomics analyses combining GC/LC-MS. Results from pyrosequencing showed a clear effect of age of kids, with more diverse bacterial community as solid feed becomes more important after weaning. A number of specific OTUs were significantly different as a result of BCM treatment of the kid at W while at W + 1 and W + 4 less OTUs were significantly changed. At W + 1, Prevotella was increased and Butyrivibrio decreased in BCM treated kids. At W + 4 only the effect of treating mothers resulted in significant changes in the abundance of some OTUs: Ruminococcus, Butyrivibrio and Prevotella. The analysis of the OTUs shared by different treatments revealed that kids at weaning had the largest number of unique OTUs compared with kids at W + 1 (137), W + 4 (238), and does (D) (23). D + k+ kids consistently shared more OTUs with mothers than the other three groups at the three sampling times. The metalobomic study identified 473 different metabolites. In does, lipid super pathway included the highest number of metabolites that were modified by BCM, while in kids all super-pathways were evenly affected. The metabolomic profile of samples from kids at W was different in composition as compared to W + 1 and W + 4, which may be directly ascribed to the process of rumen maturation and changes in the solid diet. This study shows the complexity of the bacterial community and metabolome in the rumen before weaning, which clearly differ from that after weaning and highlight the importance of the dam in transmitting the primary bacterial community after birth.

Keywords: bromochloromethane; early life; metabolome; methane; rumen.

Figure 1

Experimental design and sampling schedule.

Figure 2

Alpha diversity measures: (A) Chao1 taxonomic units estimates and (B) Shannon diversity index): W, W + 1, and W + 4). Treatment groups: D–k–= NegNeg, D–k+ =NegPos, D+k– = PosNeg, D + k+ =PosPos. ^a,bLetters denote significant differences between groups, bars that do not share the same letter are significantly different from each other (P < 0.05).

Figure 3

Principal coordinate analysis (Bray Curtis distance) comparing changes in rumen bacterial community at different times: (A) Weaning (W), (B) Weaning + 1 month (W + 1), (C) Weaning + 4 months (W + 4). Treatment groups: D–k– = NegNeg, D–k+ = NegPos, D+k– = PosNeg, D + k+ = PosPos.

Figure 4

Relative abundance of the Phyla (A) Actinobacteria, (B) Bacteroidetes, (C) Firmicutes and (D) Spirochaetes in the different experimental groups at Weaning (W), Weaning + 1 month (W + 1), and Weaning + 4 months (W + 4) time points. Treatment groups: D–k– = NegNeg, D–k+ = NegPos, D+k– = PosNeg, D + k+ = PosPos. ^a,bLetters denote significant differences between groups, bars that do not share the same letter are significantly different from each other (P < 0.05).

Figure 5

OTUs significantly different (q > 0.05 FDR) between different experimental groups at weaning. Upper and lower y-axis represents OTUs with a log2 fold positive and negative, respectively, difference for the experimental group treatment indicated above relative to treatment below. Each point represents a single OTU colored by phylum and grouped on the x axis by taxonomic genus level, size of point reflects the log2 mean abundance of the sequence data. Treatment groups: D–k– = NegNeg, D–k+ = NegPos, D+k– = PosNeg, D + k+ = PosPos.

Figure 6

Venn plots showing the OTUs across different times (W, W + 1, and W + 4) in kids (K) and mothers (M) for each experimental group: D–k–, D–k+, D+k–, D + k+.