Angela Poole
· assistant professor of Molecular NutritionVerifiedCornell University · Nutrition
Active 2002–2025
About
Angela Poole, PhD, is the Principal Investigator of the Poole Lab at Cornell University. She holds a Bachelor of Science degree in Engineering and Applied Science from the California Institute of Technology (Caltech) and earned her Doctor of Philosophy in Genome Sciences from the University of Washington. Following her doctoral studies, she completed post-doctoral research in Microbiology and Molecular Biology and Genetics at Cornell University. The Poole Lab, under her leadership, includes graduate and undergraduate students from diverse scientific backgrounds, reflecting a multidisciplinary approach to research. Contact information for Professor Poole is available through Cornell University, where she is based in the Biotechnology Building.
Research topics
- Food science
- Microbiology
- Biology
- Genetics
- Biochemistry
- Physiology
- Bioinformatics
- Ecology
- Medicine
Selected publications
medRxiv · 2025-04-01 · 1 citations
preprintOpen accessSenior authorCorrespondingAbstract The association between salivary amylase gene ( AMY1 ) copy number (CN) and metabolic health parameters, such as insulin resistance, has been studied but with conflicting results. The cause of these inconsistencies is multifaceted and confounded by differences in genotyping methods. In this study, we investigated the factors that affect the association between AMY1 CN, salivary amylase activity (SAA), and type 2 diabetes (T2D) status. We collected up to four saliva samples from two cohorts: individuals with self-reported T2D or prediabetes (n = 18) and individuals who self-reported as being without T2D or prediabetes (controls, n = 178). We genotyped individuals for AMY1 CN using both quantitative PCR and droplet digital PCR and measured SAA in the saliva samples. We demonstrated that these two commonly used methods give comparable values for AMY1 CN. We showed a positive association between the time of saliva collection and SAA throughout the day. We also observed that AMY1 CN and SAA are positively associated in individuals with and without T2D or prediabetes. With increasing AMY1 CN, SAA was higher for each additional copy of AMY1 CN in individuals with T2D or prediabetes compared to controls. Our findings support the premise that increased SAA in T2D patients is a compensatory mechanism related to the long-term protective effect of high AMY1 CN on glucose metabolism.
Circulation · 2025-11-03
article1st authorCorrespondingResistant starch (RS), a major category of dietary fiber, promotes healthy lipid and glucose metabolism. These effects are partly mediated by gut microbes. RS is known to influence microbial bile acid metabolism and, in turn, can lower serum cholesterol. We hypothesized that RS may promote another microbial process that affects serum cholesterol levels – the cholesterol:coprostanol transformation pathway, which has not been fully characterized. Individuals who harbor gut microbes encoding a recently identified gene in the pathway, intestinal sterol metabolism A (ismA), can transform cholesterol to less absorbable coprostanol. Individuals with microbial ismA genes have lower serum cholesterol than people without microbial ismA genes. We conducted a seven-week crossover study with 59 individuals completing three treatments: dietary supplementation with RS type 2, RS type 4, and a digestible starch, for ten days each with five-day washout periods in between. We collected fecal samples at the beginning and end of each treatment and extracted DNA to generate a shotgun metagenomics dataset from the gut microbiomes. We also measured the concentrations of bile acids and the sterols, cholesterol and coprostanol, in the stool. RS supplementation caused interindividual variability in gut microbiome response. Also, during the RS type 2 treatment, we observed a decrease in taurocholic acid, a bile acid that may promote colon cancer (q < 0.05). RS supplementation did not universally affect sterol levels. However, we observed consistent correlations between the abundances of some microbes, or species level genome bins (SGBs), and sterol concentrations longitudinally within subjects. We identified 24 SGBs, including three Oscillibacter species, which were negatively correlated with cholesterol and positively correlated with coprostanol (Spearman's rho ≥ 0.4). In addition to its ability to transform cholesterol, Oscillibacter has previously been implicated as benefiting lipid metabolism and cardiovascular health. We also identified 12 unclassified SGBs that may be involved in the transformation of cholesterol to coprostanol in the human gut. These SGBs may represent previously undiscovered species that participate in the cholesterol:coprostanol transformation pathway, and these species may possess unknown genes in the pathway. Comprehensive characterization of this pathway could lead to novel microbiome-based therapeutics to treat hypercholesterolemia.
The Impact of Human Salivary Amylase Gene Copy Number and Starch on Oral Biofilms
Microorganisms · 2025-02-19 · 3 citations
articleOpen accessSenior authorCorrespondingThe copy number (CN) variant AMY1 encodes the salivary amylase enzyme which promotes starch digestion. Although this gene has been associated with dental caries and periodontal disease susceptibility, the impact of the interaction between AMY1 CN and starch on oral biofilms is unclear. We explored how oral microbiota communities shaped by AMY1 CN respond to starch by employing an in vitro model of biofilm formation. We cultured biofilms using saliva samples from 31 donors with a range of AMY1 CNs (between 2 and 20 copies) and self-reported gum disease states; we used media with and without starch. Many of the most prevalent genera in saliva were also prevalent in the derived biofilms. The presence of starch in the media was associated with lower biofilm alpha diversity. We found a significant interaction between AMY1 CN and the media carbohydrate content that influenced the proportions of Atopobium and Veillonella. Members of these genera have been associated with dental caries and periodontitis. These findings suggest that the effects of carbohydrates on oral microbiome composition depend on AMY1 CN and that human oral bacteria evolved in response to expansion of this host gene locus.
PLoS ONE · 2025-07-02 · 2 citations
articleOpen accessSenior authorThe association between salivary amylase gene (AMY1) copy number (CN) and metabolic health parameters, such as insulin resistance, has been studied but with conflicting results. The etiology of these inconsistencies is multifaceted and confounded by differences in genotyping methods. In this study, we investigated the factors that affect the association between AMY1 CN, salivary amylase activity (SAA), and type 2 diabetes (T2D) status. We collected up to four saliva samples from two cohorts: individuals with self-reported T2D or prediabetes (n = 18) and individuals who self-reported as being without T2D or prediabetes (controls, n = 178). We genotyped individuals for AMY1 CN using both quantitative PCR and droplet digital PCR and measured SAA in the saliva samples. We demonstrated that these two commonly used methods give comparable values for AMY1 CN. We showed a positive association between the time of saliva collection and SAA throughout the day. We also observed that AMY1 CN and SAA are positively associated in individuals with and without T2D or prediabetes. With increasing AMY1 CN, SAA was higher for each additional copy of AMY1 CN in individuals with T2D or prediabetes compared to controls. Our findings support the premise that increased SAA in T2D patients is a compensatory mechanism related to the long-term protective effect of high AMY1 CN on glucose metabolism.
Gut Microbes · 2024 · 22 citations
Senior authorCorresponding- Biology
- Food science
- Physiology
-related metrics were not predictive of response to RS. SAA was only predictive of the relative abundance of one ASV after digestible starch supplementation. Interestingly, SCFA concentrations increased the most during digestible starch supplementation. Treatment order (the order of consumption of RS2 and RS4), alpha diversity, and a subset of ASVs were predictive of SCFA changes after RS supplementation. Based on our findings, dietary fiber intake and gut microbiome composition would be informative if assessed prior to recommending RS supplementation because these data can be used to predict changes in specific ASVs and fecal SCFA concentrations. These findings lay a foundation to support the premise that using a precision nutrition approach to optimize the benefits of dietary fibers such as RS could be an effective strategy to compensate for the low consumption of dietary fiber nationwide.
medRxiv · 2023-03-29 · 2 citations
preprintOpen accessSenior authorCorrespondingResistant starch (RS) consumption can have beneficial effects on human health, but the response, in terms of effects on the gut microbiota and host physiology, varies between individuals. Factors predicting the response to RS are not yet established and would be useful for developing precision nutrition approaches that maximize the benefits of dietary fiber intake. We sought to identify predictors of gut microbiota response to RS supplementation. We enrolled 76 healthy adults into a seven-week crossover study. Participants consumed RS type 2 (RS2), RS type 4 (RS4), and a digestible starch, for ten days each with five-day washout periods in between. We collected fecal and saliva samples and food records before and during each treatment period. We performed 16S rRNA gene sequencing and measured fecal short-chain fatty acids (SCFAs), salivary amylase gene copy number, and salivary amylase activity (SAA). Dietary fiber intake was predictive of relative abundance of several amplicon sequence variants (ASVs) at the end of both RS treatments. Treatment order (the order of consumption of RS2 and RS4), alpha diversity, and a subset of ASVs were predictive of SCFA changes after RS supplementation. SAA was only predictive of the relative abundance of ASVs after digestible starch supplementation. Based on our findings, dietary fiber intake and gut microbiome composition would be informative if assessed prior to recommending RS supplementation. Using a precision nutrition approach to optimize the benefits of dietary fibers such as RS could be an effective strategy to compensate for the low consumption of dietary fiber nationwide.
Current Developments in Nutrition · 2023-07-01
articleOpen accessSenior authorPopulation Health Management · 2023-11-27 · 1 citations
articleAccountable care organizations (ACOs) are often tasked with helping providers to deliver care efficiently and with higher quality outcomes. For an ACO to succeed in delivering efficient care, it is important to direct resources toward patients who exhibit the greatest levels of opportunity while focusing attention toward mitigating their needs. Home-based palliative care (HBPC) services are known to address patient needs for those with serious illness while decreasing the total cost of care (TCC). In this retrospective review, ACO researchers reviewed cost, quality, and utilization patterns for 3418 beneficiaries within a Medicare Shared Saving Program approaching the end of life comparing decedents who received HBPC versus those who did not receive the service. Those individuals who received HBPC services were significantly less likely to be hospitalized (51% reduction in the HBPC group), more likely to use hospice (70% vs. 43%; P = 0.001), and their TCC was less than that of those who did not receive the service ($27,203 vs. $36,089: P = 0.0163). Although more research needs to be done to understand the specific components of care delivery that are helpful in decreasing unnecessary utilization, in this retrospective review in an accountable care population, HBPC is associated with a significant decrease in cost and utilization in a population approaching end of life.
Processing and storage methods affect oral and gut microbiome composition
Frontiers in Microbiology · 2023 · 10 citations
Senior authorCorresponding- Biology
- Food science
- Microbiology
In microbiome studies, fecal and oral samples are stored and processed in different ways, which could affect the observed microbiome composition. In this study, we compared storage and processing methods applied to samples prior to DNA extraction to determine how each affected microbial community diversity as assessed by 16S rRNA gene sequencing. We collected dental swabs, saliva, and fecal samples from 10 individuals, with three technical replicates per condition. We assessed four methods of storing and processing fecal samples prior to DNA extraction. We also compared different fractions of thawed saliva and dental samples to fresh samples. We found that lyophilized fecal samples, fresh whole saliva samples, and the supernatant fraction of thawed dental samples had the highest levels of alpha diversity. The supernatant fraction of thawed saliva samples had the second highest evenness compared to fresh saliva samples. Then, we investigated the differences in observed community composition at the domain and phylum levels and identified the amplicon sequence variants (ASVs) that significantly differed in relative abundance between the conditions. Lyophilized fecal samples had a greater prevalence of Archaea as well as a greater ratio of Firmicutes to Bacteroidetes compared to the other conditions. Our results provide practical considerations not only for the selection of storage and processing methods but also for comparing results across studies. Differences in processing and storage methods could be a confounding factor influencing the presence, absence, or differential abundance of microbes reported in conflicting studies.
Processing and Storage Methods Affect Oral and Gut Microbiome Composition
bioRxiv (Cold Spring Harbor Laboratory) · 2023 · 1 citations
Senior authorCorresponding- Biology
- Food science
- Microbiology
Across microbiome studies, fecal and oral samples are stored and processed in different ways, which could affect the observed microbiome composition. Here, we compared treatment methods, which included both storage conditions and processing methods, applied to samples prior to DNA extraction to determine how each affects microbial community diversity as assessed by 16S rRNA gene sequencing. We collected dental swab, saliva, and fecal samples from 10 individuals, with three technical replicates per treatment method. We assessed four methods of processing fecal samples prior to DNA extraction. We also compared different fractions of frozen saliva and dental samples to fresh samples. We found that lyophilized fecal samples, fresh whole saliva samples, and the supernatant fraction of thawed dental samples retained the highest levels of alpha diversity in samples. The supernatant fraction of thawed saliva samples had the second highest alpha diversity compared to fresh. Then we investigated the differences in microbes between different treatments at the domain and phylum levels as well as identified the amplicon sequence variants (ASVs) that were significantly different between the methods producing the highest alpha diversity and the other treatment methods. Lyophilized fecal samples had a greater prevalence of Archaea as well as a greater ratio of Firmicutes to Bacteroidetes compared to the other treatment methods. Our results provide practical considerations, not only for selection of processing method, but also for comparing results across studies that use these methods. Our findings also indicate differences in treatment method could be a confounding factor influencing the presence, absence, or differential abundance of microbes reported in conflicting studies.
Frequent coauthors
- 17 shared
Ruth E. Ley
Max Planck Institute for Biology
- 12 shared
Julia K. Goodrich
Massachusetts General Hospital
- 11 shared
Lynn M. Johnson
Statistical Research (United States)
- 6 shared
Jessica L. Sutter
Max Planck Institute for Developmental Biology
- 5 shared
Selina Yu
University of Puget Sound
- 5 shared
Jillian L. Waters
Bay Institute
- 4 shared
Leo J. Pallanck
University of Washington
- 4 shared
Guillermo G. Luque
Max Planck Institute for Biology
Labs
Education
B.S., Engineering and Applied Science
California Institute of Technology (Caltech)
Awards & honors
- NIH Early Career Reviewer Program, study section: Nutrition…
- USDA NIFA grant review panel, study section on Food and Huma…
- Associate Editor on the Editorial Board of Microbiome in Hea…
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