Add metagenomics paper

content/academia/metagenomics/index.md

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+---
+title: "Metagenomic analysis of rumen populations in week-old calves as altered by maternal late gestational nutrition and mode of delivery"
+date: 2019-06-12
+cardImage: cannulated-cows
+draft: false
+featured: true
+keywords:
+  - gestation
+  - metagenomics
+  - microbiome
+  - rumen
+type: "Poster"
+authors:
+  - T. A. Christensen II
+  - K. J. Austin
+  - K. M. Cammack
+  - H. C. Cunningham-Hollinger
+link: 'https://dx.doi.org/...'
+journal: "Westion Section American Society of Animal Science Annual Meeting"
+location: "Boise, Idaho"
+awards:
+  - '1st Place Undergraduate Poster Competition'
+---
+
+Early colonization of the rumen microbiome is critical to host health and long
+term performance. Factors that influence early colonization include maternal
+factors such as gestational nutrition and mode of delivery. Therefore, we
+hypothesized that late gestational nutrition and mode of delivery would
+influence the calf rumen microbiome. Our objectives were to determine if
+nutrient restriction during late gestation alters the calf rumen microbiome and
+determine if ruminal microbiome composition differs in calves born vaginally
+versus caesarean. Late gestating Angus cows were randomly allocated to one of
+three treatment groups: control (**CON**; n = 6), caesarean section (**CS**; n =
+4), and nutrient restricted (**NR**; n = 5), where CON were fed DDGS and hay to
+meet NRC requirements and calved naturally; CS were fed similarly to CON and
+calves were born via caesarean section; and NR were fed at a level to reduce BCS
+by 1.5-2.0 points over the last trimester compared to CON and calved naturally.
+Rumen fluid was collected via oral lavage prior to partition from cows and at d
+7 from calves. Microbial DNA was isolated from the rumen fluid and metagenomic
+shotgun sequencing was performed using the Illumina HiSeq 2500 platform.
+Sequence data were analyzed using Metaxa2 for taxonomic assignment followed by
+QIIME1 and QIIME2 to determine differential abundance and alpha- and
+beta-diversity differences. There were no significant differences in
+alpha-diversity as measured by shannon index across treatment groups for cows
+(_P_ = 0.239), but there were significant differences for calves (_P_ = 0.015).
+Similarly, there were no significant differences in beta-diversity as measured
+by the bray-curtis dissimilarity matrix for cows (_P_ = 0.059), but there were
+significant differences for calves (_P_ = 0.007). Alpha-diversity differed (_P_
+< 0.001) between cows and calves, with cows having increased species richness
+compared to calves. Beta-diversity also differed (_P_ = 0.001) between cows and
+calves. At total of 410 taxa were differentially abundant (_P_ < 0.01) between
+cows and calves. These results suggest that the mature rumen microbiome of cows
+is able to withstand changes in feed intake, however the calf microbiome is
+susceptible to alteration by maternal factors. These data also suggest that
+there may be opportunities to develop management strategies during late
+gestation that influence calf health and performance long-term.