Weimer, P. J. | Search bioRxiv

bioRxiv2018

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

The characterization of microbial communities by metagenomic approaches has been enhanced by recent improvements in short-read sequencing efficiency and assembly algorithms. We describe the results of adding long-read sequencing to the mix of technologies used to assemble a highly complex cattle rumen microbial community, and compare the assembly to current short read-based methods applied to the same sample. Contigs in the long-read assembly were 7-fold longer on average, and contained 7-fold more complete open reading frames (ORF), than the short read assembly, despite having three-fold lower sequence depth. The linkages between long-read contigs, provided by proximity ligation data, supported identification of 188 novel viral-host associations in the rumen microbial community that suggest cross-species infectivity of specific viral strains. The improved contiguity of the long-read assembly also identified 94 antimicrobial resistance genes, compared to only seven alleles identified in the short-read assembly. Overall, we demonstrate a combination of experimental and computational methods that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

microbiology↗

bioRxiv2018

Diet influences early microbiota development in dairy calves without long-term impacts on milk production

Gastrointestinal tract (GIT) microorganisms play important roles in the health of ruminant livestock and impact production of agriculturally relevant products, including milk and meat. Despite this link, interventions to alter the adult microbiota to improve production have proven ineffective as established microbial communities are resilient to change. In contrast, developing communities in young animals may be more easily altered but are less well-studied. Here, we measured the GIT-associated microbiota of 45 Holstein dairy cows from 2 weeks to first lactation using Illumina amplicon sequencing of bacterial (V4 16S), archaeal (V6-8 16S), and fungal (ITS1) communities. Fecal and rumen microbiota were correlated to growth and milk production of animals raised on calf starter grains and/or corn silage to determine if early-life diet has long-term impacts. Significant diet-associated differences in total microbial communities and specific taxa were observed by weaning (8 weeks), but all animals reached an adult-like composition between weaning and 1-year. While some calf diet-driven differences were apparent in the microbiota of adult cows, these dissimilarities did not correlate with animal growth or milk production. This suggests that initial microbial community establishment is impacted by early-life diet, but post-weaning factors have a greater influence on adult communities and production outcomes.\n\nSIGNIFICANCEThe gut microbiota is essential to the survival of many organisms, including ruminants that rely on microorganisms for nutrient acquisition from dietary inputs toward the production of products like milk and meat. While alteration of the adult ruminant microbiota to improve production is possible, changes are often unstable and fail to persist. In contrast, the early-life microbiota may be more amenable to sustained modification; however, few studies have determined the impacts of early-life interventions on downstream production. Here, we investigated the impacts of agriculturally relevant calf diets, including calf starter and corn silage, on gut microbial communities, animal growth, and production through the first lactation cycle. Thus, this work serves to further our understanding of early-life microbiota acquisition as well as informs future practices in livestock management.

microbiology↗