Biology subjects

Baxter, N. T.

Publications and source records attributed to Baxter, N. T..

3 recordsLinked to original sources

bioRxiv2022

Interactions between time on diet, antibiotic treatment, and liver abscess development on the fecal microbiome of beef cattle

Liver abscesses caused by polymicrobial infections of the liver are a widespread problem in feedlot cattle production. There are currently no effective methods for the early detection of liver abscesses or to predict antibiotic efficacy. Although gene expression and microbiome differences have been reported in the rumen of abscessed and normal animals, liver abscess biomarkers using less invasive tools can facilitate managing of the disease in the field. Here we report the results of two studies measuring the fecal microbiome composition of steers that did or did not develop liver abscesses, with or without antibiotic treatment, along a 7-month feeding period on a high-concentrate diet. Our results indicate a limited impact of liver abscesses or tylosin on fecal microbiome composition, with time on diet explaining most variance in the fecal microbiome. Interestingly, in both studies, antibiotic treatment led to larger differences in both the composition and variance of the fecal microbiomes between abscessed and normal animals compared to controls. These differences were limited to specific sampling times in each of the two studies. Although multiple amplicon sequence variants with differential abundances according to liver abscess state were identified, there was no overlap between the two studies. Our results suggests that early fecal biomarkers of liver abscess susceptibility might be developed, especially for animals receiving preventative antibiotics, but the fecal abundance of individual microorganisms may not be a robust predictor across different sampling times or diet regimes.

microbiology↗

bioRxiv2018

Dynamics of human gut microbiota and short-chain fatty acids in response to dietary interventions with three fermentable fibers

Production of short-chain fatty acids (SCFAs), especially butyrate, in the gut microbiome is required for optimal health but is frequently limited by the lack of fermentable fiber in the diet. We attempted to increase butyrate production by supplementing the diets of 174 healthy young adults for two weeks with resistant starch from potatoes (RPS), resistant starch from maize (RMS), inulin from chicory root, or an accessible corn starch control. RPS resulted in the greatest increase in total SCFAs, including butyrate. Although the majority of microbiomes responded to RPS with increases in the relative abundance of bifidobacteria, those that responded with an increase in Ruminococcus bromii or Clostridium chartatabidum were more likely to yield higher butyrate concentrations, especially when their microbiota were replete with populations of the butyrate-producing species Eubacterium rectale. RMS and inulin induced different changes in fecal communities, but they did not generate significant increases in fecal butyrate levels.\n\nIMPORTANCEThese results reveal that not all fermentable fibers are equally capable of stimulating SCFA production, and they highlight the importance of the composition of an individuals microbiota in determining whether or not they respond to a specific dietary supplement. In particular, R. bromii or C. chartatabidum may be required for enhanced butyrate production in response to RS. Bifidobacteria, though proficient at degrading RS and inulin, may not contribute to the butyrogenic effect of those fermentable fibers in the short term.

microbiology↗

bioRxiv2017

The effect of treatment on the microbiota of patients diagnosed with colonic lesions

BackgroundColorectal cancer is a worldwide health problem. Despite growing evidence that members of the gut microbiota can drive tumorigenesis, little is known about what happens to it after treatment for an adenoma or carcinoma. This study tested the hypothesis that treatment for adenoma or carcinoma alters the abundance of bacterial populations associated with disease to those associated with a normal colon. We tested this hypothesis by sequencing the 16S rRNA genes in the feces of 67 individuals before and after treatment for adenoma (N = 22), advanced adenoma (N = 19), and carcinoma (N = 26).\n\nResultsThere were small changes to the bacterial community associated with adenoma or advanced adenoma and large changes associated with carcinoma. The communities from patients with carcinomas changed significantly more than those with adenoma following treatment (P-value < 0.001). Although treatment was associated with intrapersonal changes, the change in the abundance of individual OTUs in response to treatment was not consistent within diagnosis groups (P-value > 0.05). Because the distribution of OTUs across patients and diagnosis groups was irregular, we used the Random Forest machine learning algorithm to identify groups of OTUs that could be used to classify pre and post-treatment samples for each of the diagnosis groups. Although the three models could differentiate between the pre and post-treatment samples, there was little overlap between the OTUs that were indicative of each treatment. To determine whether individuals who underwent treatment were more likely to have OTUs associated with normal colons we used a larger cohort that contained individuals with normal colons and those with adenomas, advanced adenomas, and carcinomas. We again built Random Forest models and measured the change in the positive probability of having one of the three diagnoses to assess whether the post-treatment samples received the same classification as the pre-treatment samples. Samples from patients who had carcinomas changed towards a microbial milieu that resembles the normal colon after treatment (P-value < 0.05). Finally, we were unable to detect any significant differences in the microbiota of individuals treated with surgery alone and those treated with chemotherapy or chemotherapy and radiation (P-value > 0.05).\n\nConclusionsBy better understanding the response of the microbiota to treatment for adenomas and carcinomas, it is likely that biomarkers will eventually be validated that can be used to quantify the risk of recurrence and the likelihood of survival. Although it was difficult to identify significant differences between pre and post-treatment samples from patients with adenoma and advanced adenoma, this was not the case for carcinomas. Not only were there large changes in pre versus post-treatment samples for those with carcinoma, but these changes were towards a more normal microbiota.

microbiology↗