Evaluation of the liver abscess microbiome and liver abscess prevalence in cattle reared for production of natural branded beef

Transcription

1 Evaluation of the liver abscess microbiome and liver abscess prevalence in cattle reared for production of natural branded beef K.L. Huebner, J.N. Martin C.J. Weissend, K.L. Holzer, M. Weinroth, Z. Abdo, J.L. Metcalf, I. Geornaras, J.K. Parker, P.S. Morley, K.E Belk

2 Liver abscesses are primary cause of liver condemnation at slaughter Abscess rate highly variable (10 20%) Tylosin fed to reduce abscesses Fed to 72% of cattle on head feedlots in US Polymicrobial Infections Fusobacterium necrophorum Trueperella pyogenes S l ll i

3 Pathogenesis Nagaraja and Lechtenberg. Vet Clin Food Anim Brown and Lawrence. J. Anim. Sci Severe abscesses have greatest effect on carcass value

4 Objective: To evaluate the flora of liver abscesses in naturally raised finishing beef steers using 16S ribosomal RNA marker genes. Image: IBDrelief.com

5 16S rrna Sequencing Metagenomics emerged in response to the observation that most micro organisms can t be cultured ~85% non culturable The rrna gene contains conserved areas that enable amplification using PCR and a hypervariable region that enables genotyping of bacteria without culture Offers increased sampling of bacterial diversity per $ spent ~$20 50/sample Allows snapshot of taxonomic diversity Not as specific for species and strain Identification Handelsman et al. Chem & Biol. 1998

6 Materials and Methods Certified natural cattle (no antimicrobials or growth hormones) from a Colorado feedlot Liver abscess rates and grade 4,323 individual animals as part of a randomized trial. Blocked on weight and randomized to two pens within a pen block Cattle sourced similar relative to pen block Harvested in late September through January 33 liver abscess samples 13 pens, 7 pen blocks of 2 adjacent pens (shared border) One to five liver abscesses per pen Bacterial community (microbiome) characterized Aerial Image of a Feedlot (Google Earth image)

7 Liver abscess scores collected on individual animals at slaughter Two pens made up one pen block. Seven pen blocks were sampled from a Colorado feedlot raised for natural branded beef products Sterile extraction of purulent material Image source: Elanco Liver check

8 Bioinformatic analysis DNA Isolation Trimming and quality filtering Open Reference OTU picking Sequence clustering (UCLUST) Taxonomy assignment (Greengenes) database DNA Quantification/Quality Control 16S Library Preparation Illumina sequencing by synthesis Image source:novogene. Image source:illumina.

9 Results

10 Phylum level taxonomic summary by pen blocks (PB) of cattle. PB1 PB2 PB3 PB4 PB6 PB7 PB9 100% ~ 81 genera were detected More variability and diversity than we previously thought Variation within a feedlot substantial 80% 60% 40% 20% 0% Fusobacteria Firmicutes Actinobacteria Chloroflexi Nitrospirae Armatimonadetes Tenericutes k Bacteria;p Tenericutes Bacterioidetes k Archaea;p Crenarchaeota Proteobacteria Acidobacteria k Bacteria;p Armatimonadetes Chlorobi k Bacteria;p Planctomycetes k Bacteria;p Nitrospirae Planctomycetes k Bacteria;p Gemmatimonadetes Gemmatimonadetes Crenarchaeota Each pen block represents two pens of cattle housed adjacent to each other in the feedlot during the entire finishing period.

11 Principle Components Plot based on unweighted Unifrac distances for bacteria of liver abscess microbiome plotted on total liver abscess rate gradient PC1=55% PC2=15% Total abscess rate Each pen block represents two pens of cattle housed adjacent to each other in the feedlot during the entire finishing period. Correlation between abscess rate and pen block microbiome OTU differences in the genus, Fusobacterium, are driving some of the differences in clustering by abscess rate and pen block.

12 High liver abscess prevalence : 38.5% Liver abscesses very diverse polymicrobial communities Clustering by pen block within feedlot Variation within feedlot of liver abscess microbiome Location in feedlot or cattle source as possible drivers? 16S rrna analysis methods effective at capturing bacterial diversity and ecology in liver abscess samples of beef cattle.

13 Future Directions Understanding how the liver abscess microbiome is related to changes in feedlot management, including diet, feed additives, antimicrobial use, and geographical differences in the soil microbiome. Further comparison to culture methods

14 Acknowledgements Funding for this project was provided by the National Cattlemen s Beef Association. Thank you to our collaborators from JBS Five Rivers, and Diamond T. Also thank you to the CSU Animal Science graduate students.