Browsing by Author "Olivo, Sarah K."

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Biogeographical Differences in the Influence of Maternal Microbial Sources on the Early Successional Development of the Bovine Neonatal Gastrointestinal tract
(2018-02) Yeoman, Carl J.; Ishaq, Suzanne L.; Bichi, Elena; Olivo, Sarah K.; Lowe, James; Aldridge, Brian M.
The impact of maternal microbial influences on the early choreography of the neonatal calf microbiome were investigated. Luminal content and mucosal scraping samples were collected from ten locations in the calf gastrointestinal tract (GIT) over the first 21 days of life, along with postpartum maternal colostrum, udder skin, and vaginal scrapings. Microbiota were found to vary by anatomical location, between the lumen and mucosa at each GIT location, and differentially enriched for maternal vaginal, skin, and colostral microbiota. Most calf sample sites exhibited a gradual increase in α-diversity over the 21 days beginning the first few days after birth. The relative abundance of Firmicutes was greater in the proximal GIT, while Bacteroidetes were greater in the distal GIT. Proteobacteria exhibited greater relative abundances in mucosal scrapings relative to luminal content. Forty-six percent of calf luminal microbes and 41% of mucosal microbes were observed in at-least one maternal source, with the majority being shared with microbes on the skin of the udder. The vaginal microbiota were found to harbor and uniquely share many common and well-described fibrolytic rumen bacteria, as well as methanogenic archaea, potentially indicating a role for the vagina in populating the developing rumen and reticulum with microbes important to the nutrition of the adult animal.
Feed efficiency phenotypes in lambs involve changes in ruminal, colonic, and small-intestine-located microbiota
(2017-06) Perea, K.; Perz, Katharine A.; Olivo, Sarah K.; Williams, Andrew F.; Lachman, Medora M.; Ishaq, Suzanne L.; Thomson, Jennifer M.; Yeoman, Carl J.
Several studies have revealed differences in rumen-located microbes between greatly efficient and inefficient animals; however, how the microbiota vary in the hind gastrointestinal tract (GIT) has only been sparsely explored and how they vary in the small intestine remains to be determined. We therefore sampled the microbiota of the duodenum, jejunum, ileum, colon, and colorectally-obtained feces, in addition to the rumen of 12 lambs that, in a residual feed intake trial, were found to be at either extreme of feed efficiency phenotypes. The 16S rRNA gene (V3-V4 region) profiles of all samples were analyzed and revealed unique microbiota in all GIT locations except the jejunum and ileum (ANOSIM R > 0.2, P < 0.001). Measures of beta-diversity revealed greater dissimilarity between more anatomically distant GIT locations (e.g., Rumen-Duodenum, ANOSIM R = 0.365, P < 0.001; Rumen-Colon, ANOSIM R = 1, P < 0.001) with the nearest distal region typically more similar than the nearest proximal location. The relative abundances of 13 operational taxonomic units (OTUs) from the duodenum, jejunum, colon, and feces, as well as the rumen, differed between efficient and inefficient animals (Bonferroni corrected, P < 0.05), while another 2 OTUs trended toward significance. These OTUs were classified as taxa with known roles in fibrolysis (Fibrobacteres, Ruminococcaceae, and Saccharofermentans) and others that are commonly associated with health (Bifidobacteriaceae, and Christensenellaceae) and dysbiosis (Proteobacteria). Our findings show biospatial delineations of microbiota throughout the GIT and suggest that feed efficiency extends beyond the rumen, transcending these regions, and involves increases in both rumen-and colon-located fibrolytic taxa, increases in bifidobacterial species in the small intestine, and reductions in small intestine and distal GIT-located Proteobacteria.
Impact of Cropping Systems, Soil Inoculum, and Plant Species Identity on Soil Bacterial Community Structure
(2017-02) Ishaq, Suzanne L.; Johnson, Stephen P.; Miller, Zachariah J.; Lehnhoff, Erik A.; Olivo, Sarah K.; Yeoman, Carl J.; Menalled, Fabian D.
Farming practices affect the soil microbial community, which in turn impacts crop growth and crop-weed interactions. This study assessed the modification of soil bacterial community structure by organic or conventional cropping systems, weed species identity [Amaranthus retroflexus L. (redroot pigweed) or Avena fatua L. (wild oat)], and living or sterilized inoculum. Soil from eight paired USDA-certified organic and conventional farms in north-central Montana was used as living or autoclave-sterilized inoculant into steam-pasteurized potting soil, planted with Am. retroflexus or Av. fatua and grown for two consecutive 8-week periods to condition soil nutrients and biota. Subsequently, the V3-V4 regions of the microbial 16S rRNA gene were sequenced by Illumina MiSeq. Treatments clustered significantly, with living or sterilized inoculum being the strongest delineating factor, followed by organic or conventional cropping system, then individual farm. Living inoculum-treated soil had greater species richness and was more diverse than sterile inoculum-treated soil (observed OTUs, Chao, inverse Simpson, Shannon, P<0.001) and had more discriminant taxa delineating groups (linear discriminant analysis). Living inoculum soil contained more Chloroflexi and Acidobacteria, while the sterile inoculum soil had more Bacteroidetes, Firmicutes, Gemmatimonadetes, and Verrucomicrobia. Organically farmed inoculum-treated soil had greater species richness, more diversity (observed OTUs, Chao, Shannon, P<0.05), and more discriminant taxa than conventionally farmed inoculum-treated soil. Cyanobacteria were higher in pots growing Am. retroflexus, regardless of inoculum type, for three of the four organic farms. Results highlight the potential of cropping systems and species identity to modify soil bacterial communities, subsequently modifying plant growth and crop-weed competition.