Science Advances

Supplementary Materials

The PDF file includes:

  • Supplementary Materials and Methods
  • Supplementary Text. Interactions between main categories of ruminal microbes in abundance, diversity, and animal phenotype.
  • Fig. S1. Rank abundance plot for core microbes along farms.
  • Fig. S2. Overview of genetic components along the Holstein cohort and host SNP-microbe association effort.
  • Fig. S3. Microbial species interaction within and between domains.
  • Fig. S4. Species richness and abundance of rumen microbial domains reveal ecological interactions and connection to host traits.
  • Fig. S5. Host genetics, core microbiome composition, and diet shape the host phenotypic landscape.
  • Fig. S6. Heritable microbes tend to explain experimental variables better in comparison to nonheritable core microbes.
  • Fig. S7. Explained variation (r2) of different host traits as function of core microbiome composition, according to RF prediction model.
  • Fig. S8. The vast majority of core microbes do not show a seasonal association, and evidence for seasonality usually does not repeat in more than one farm.
  • Table S1. Average diet formulations and composition on each farm.
  • Table S2. Conditions for quantitative PCR.
  • Legends for data S1 to S10
  • References (6770)

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Other Supplementary Material for this manuscript includes the following:

  • Data S1 (Microsoft Excel format). Animals used in the experiment together with diet, measured phenotypes, and other experimental variables.
  • Data S2 (Microsoft Word format). Presence of bacterial taxonomic groups that were found to be most abundant in Henderson et al. (6) and appear also in the current study.
  • Data S3 (Microsoft Word format). Presence of archaeal taxonomic groups that were found to be most abundant in Henderson et al. (6) and appear also in the present study.
  • Data S4 (Microsoft Word format). Presence of protozoal taxonomic groups that were found to be most abundant in Henderson et al. (6) and appear also in the present study.
  • Data S5 (Microsoft Excel format). Summary of abundance and occupancy of the core microbial species (prokaryotes, fungi, and protozoa).
  • Data S6 (Microsoft Excel format). Heritable microbes.
  • Data S7 (Microsoft Excel format). Microbes associated with phenotypic traits.
  • Data S8 (Microsoft Excel format). Closest representative sequenced genomes for heritable microbes.
  • Data S9 (Microsoft Excel format). Season-affected microbes.
  • Data S10 (.zip format). Animal genotypes (SNP values).

Files in this Data Supplement: