Molecular, Genetic, and Biochemical Nutrition Commons^™

Development Of Databases For Glycan Utilization And Anti-Prokaryotic Defense In Microbiomes, Yuchen Yan

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Microbiomes in humans, animals, plants, and other environments are necessary components of the biosphere for global nutrient cycling and maintaining ecosystem balance. In particular, the gut microbiome plays an essential role in modulating human health through glycan utilization. Carbohydrate-active enzymes (CAZymes), CAZyme gene clusters (CGCs), and polysaccharide utilization loci (PULs) are key genomic features that determine microbial capacities for carbohydrate metabolism. Meanwhile, the arms race between phages and prokaryotes has led to the evolution of various anti-prokaryotic immune systems (APIS) in phages to counteract prokaryotic immune systems (PIS).

As bioinformatics methods used to analyze microbiome information advance rapidly, there is …

The Role Of Peroxisomal Acot4 And Acot8 In Modulating Lipid Metabolism And Stress Pathways In Steatotic Hepatocytes, Sylwia Miekus

Department of Nutrition and Health Sciences: Dissertations, Theses, and Student Research

Metabolic dysfunction-associated steatotic liver disease (MASLD) is characterized by excessive lipid accumulation in hepatocytes and the development of lipotoxic stress that disrupts cellular homeostasis. Peroxisomal lipid metabolism plays an important role in maintaining acyl-CoA balance during fatty acid overload, yet the contribution of peroxisomal acyl-CoA thioesterases to early lipotoxic responses remains insufficiently understood. The aim of this study was to investigate the functional involvement of the peroxisomal enzymes acyl-CoA thioesterase 4 (ACOT4) and acyl-CoA thioesterase 8 (ACOT8) in hepatocyte lipid handling under acute lipotoxic conditions. An in vitro model of steatosis was established in AML12 cells through exposure to a …

Improved Rumen Microbiome Interpretation Via Empirical Filtration Derived From Known Mock Microbiomes, Wesley A. Tom

School of Biological Sciences: Dissertations, Theses, and Student Research

The rumen microbiome plays a critical role in ruminant health and performance. As a consequence, many studies investigate microbial community composition using 16S rDNA based sequencing. As such, data quality and data filtering are critical to accurately identify microbial community composition. In this study we use mock communities to empirically select data filtering parameters to reduce artifact populations and compared the effect of filtering using different bioinformatic pipelines using rumen bacterial community data. The filtering parameters identified provides consistent estimates of rumen microbial diversity, regardless of bioinformatic pipeline utilized and provides a more accurate view of microbiome structure and composition. …

The Effect Of Diet Formulations Containing Different Protein Sources On Energy And Nitrogen Utilization In Lactating Jersey Cows, Kortney Ann Harpestad

Department of Animal Science: Dissertations, Theses, and Student Research

It is well understood that lactating dairy cows require metabolizable protein (MP) for milk yield and milk protein synthesis. Diets with conventional feed sources like corn and soybean meal (SBM) may not sufficiently meet all MP and amino acid (AA) requirements so supplementation with more rumen undegradable protein (RUP) rich feeds or rumen-protected AA can be fed to support animal performance. The growth trajectory of biofuels has resulted in dramatic increases in the production of feeds like heat treated soybean meal (HTSBM). While the chemical composition of this product is understood, there is a need to better understand how HTSBM …

Increasing The Impact Of Dietary Fiber From Grains On Human Health Through Gut Microbiome, Sujun Liu

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The relationship between dietary fiber intake and human health has gained significant attention due to its potential in preventing chronic diseases and promoting gut health. Grains are a primary source of dietary fiber; however, the health impact of grain fibers is often limited because they are incompletely metabolized by gut bacteria. This dissertation explores innovative strategies to enhance the concentration and of dietary fiber from grains and its utilization by gut bacteria. By investigating various treatments, this research aims to maximize the health benefits of grain-derived dietary fibers, thereby contributing to a healthier society.

This dissertation is organized into four …

Overall And Sex-Specific Associations Of Serum Lipid-Soluble Micronutrients With Metabolic Dysfunction-Associated Steatotic Liver Disease Among Adults In The United States, Weiwen Chai, Meng-Hua Tao

Department of Nutrition and Health Sciences: Faculty Publications

This study examined overall and sex-specific associations of serum lipid-soluble micronutrients including α- and γ-tocopherols, 25-hydroxy-vitamin D (25(OH)D), retinol, and six major carotenoids with metabolic dysfunction-associated steatotic lever disease (MASLD) using the 2017–2018 National Health and Nutrition Examination Survey. This analysis included 3956 adults (1991 men, 1965 women) aged ≥ 20 years. Steatotic liver disease was determined through transient elastography examination. Odds ratios (ORs) and 95% confidence intervals (95% CIs) for MASLD associated with micronutrients were estimated using logistic regressions. Higher serum α-tocopherol (highest vs. lowest quartile: OR = 1.53, 95% CI = 1.05–2.22, p = 0.03) and γ-tocopherol (highest …

Association Of Habitual Intake Of Probiotic Supplements And Yogurt With Characteristics Of The Gut Microbiome In The Multiethnic Cohort Adiposity Phenotype Study, Weiwen Chai, Gertraud Maskarinec, Unhee Lim, Carol J. Boushey, Lynne R. Wilkens, V. Wendy Setiawan, Loïc Le Marchand, Timothy W. Randolph, Isaac C. Jenkins, Johanna W. Lampe, Meredith A.J. Hullar

Department of Nutrition and Health Sciences: Faculty Publications

Consumption of probiotics and/or yogurt could be a solution for restoring the balance of the gut microbiota. This study examined associations of regular intake of probiotic supplements or yogurt with the gut microbiota among a diverse population of older adults (N=1,861; 60–72 years). Fecal microbial composition was obtained from 16S rRNA gene sequencing (V1-V3 region). General Linear Models were used to estimate the associations of probiotic supplement or yogurt intake with microbiome measures adjusting for covariates. Compared to non-yogurt consumers (N=1,023), regular yogurt consumers (≥once/week, N=818) had greater Streptococcus (β=0.29, P=0.0003) and lower Odoribacter (β=−0.33, P<0.0001) abundance. The directions of the above associations were consistent across the five ethnic groups but stronger among Japanese Americans (Streptococcus: β=0.56, P=0.0009; Odoribacter: …

The Impact Of Iron Supplementation On The Preterm Neonatal Gut Microbiome: A Pilot Study, Matthew Van Ormer, Maranda Thompson, Melissa K. Thoene, Jean-Jack Riethoven, Sathish Kumar Natarajan, Ann Anderson-Berry

Department of Nutrition and Health Sciences: Faculty Publications

Objective The gastrointestinal microbiome in preterm infants exhibits significant influence on optimal outcomes–with dysbiosis shown to substantially increase the risk of the life-threatening necrotizing enterocolitis. Iron is a vital nutrient especially during the perinatal window of rapid hemoglobin production, tissue growth, and foundational neurodevelopment. However, excess colonic iron exhibits potent oxidation capacity and alters the gut microbiome–potentially facilitating the proliferation of pathological bacterial strains. Breastfed preterm infants routinely receive iron supplementation starting 14 days after delivery and are highly vulnerable to morbidities associated with gastrointestinal dysbiosis. Therefore, we set out to determine if routine iron supplementation alters the preterm gut …

Increasing Maternity Leave And Decreasing Attrition Rates Of U.S. Active Duty Women In The Prenatal And Immediate Postpartum Period, Minette S.R. Herrick, Weiwen Chai

Department of Nutrition and Health Sciences: Faculty Publications

Introduction:The USA currently does not have a national parental leave policy. In 2016, the Secretary of Defense increased the allotted maternity leave for active duty U.S. military members from 6 to 12 weeks. The purpose of this study was to understand the potential impact of this change on attrition rates of active duty women in the Army, Air Force, Navy, and Marines from their initial prenatal visit through the first year postpartum.

Methods: All active duty women who had a confirmed pregnancy in the electronic health record from 2011 to 2019 were included for consideration in the study. …

Characterization And Evaluation Of Bioactivity Of Dry Edible Bean And Bean Derived Small Peptides, Bikram Prasad Upadhyaya

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Obesity, diabetes, and their metabolic complications continue to be one of the major global public health concerns with a few effective treatment options. Although regular exercise and a well-balanced diet that includes calories from pulses can be recommended, much remains to be elucidated about the health effects of the various bioactive compounds including peptides and polyphenols present in pulses. Most of the previous studies have focused on individual dietary compounds and only a few investigated the synergistic effect of active compounds in modulating human health. Hence this dissertation aimed first, to provide a comparative evaluation of the overall therapeutic value …

Milk-Borne Small Extracellular Vesicles: Kinetics And Mechanisms Of Transport, Distribution, And Elimination, Alice Ngu, Javaria Munir, Janos Zempleni

Department of Nutrition and Health Sciences: Faculty Publications

Small extracellular vesicles (sEVs) in milk have the qualities desired for delivering therapeutics to diseased tissues. The production of bovine milk sEVs is scalable (10²¹ annually per cow), and they resist degradation in the gastrointestinal tract. Most cells studied to date internalize milk sEVs by a saturable process that follows Michaelis-Menten kinetics. The bioavailability of oral milk sEVs is approximately 50%. In addition to crossing the intestinal mucosa, milk sEVs also cross barriers such as the placenta and blood-brain barrier, thereby enabling the delivery of therapeutics to hard-to-reach tissues. In time course studies, levels of milk sEVs peaked in …

Kluyveromyces Marxianus Prepared As A Ready To Use Supplemental Food (Rusf), Zachary Christman

Applied Science Program: Theses

Ready to Use Supplemental Food (RUSF) is a nutrient dense paste or compressed bar used to supplement a person’s nutritional needs because of malnutrition or due to food shortages. The purpose of this article is to demonstrate some methods of how the dairy organism Kluyveromyces marxianus can be used to enrich the protein value of bread or ferment a substrate such as wheat bran into a more digestible form.

Resistance Training In Humans And Mechanical Overload In Rodents Do Not Elevate Muscle Protein Lactylation, Madison L. Mattingly, Auburn University A. Ruple, Casey L. Sexton, Joshua S. Godwin, Mason C. Mcintosh, Morgan A. Smith, Daniel L. Plotkin, J. Max Michel, Derick A. Anglin, Nicholas J. Kontos, Shengyi Fei, Stuart M. Phillips, C. Brooks Mobley, Ivan Jose Vechetti Jr, Christopher G. Vann, Michael D. Roberts

Department of Nutrition and Health Sciences: Faculty Publications

Although several reports have hypothesized that exercise may increase skeletal muscle protein lactylation, empirical evidence in humans is lacking. Thus, we adopted a multifaceted approach to examine if acute and subchronic resistance training (RT) altered skeletal muscle protein lactylation levels. In mice, we also sought to examine if surgical ablation-induced plantaris hypertrophy coincided with increases in muscle protein lactylation. To examine acute responses, participants’ blood lactate concentrations were assessed before, during, and after eight sets of an exhaustive lower body RT bout (n = 10 trained college-aged men). Vastus lateralis biopsies were also taken before, 3-h post, and 6-h post-exercise …

Critical Contributions Of Protein Cargos To The Functions Of Macrophage‑Derived Extracellular Vesicles, Baolong Liu, Phuong Linh Nguyen, Han Yu, Xingzhi Li, Huiren Wang, Wang Price, Meng Niu, Chittibabu Guda, Xiao Cheng, Xinghui Sun, Regis Moreau, Amanda E. Ramer-Tait, Michael J. Naldrett, Sophie Alvarez, Jiujiu Yu

Department of Nutrition and Health Sciences: Faculty Publications

Background Macrophages are highly plastic innate immune cells that play key roles in host defense, tissue repair, and homeostasis maintenance. In response to divergent stimuli, macrophages rapidly alter their functions and manifest a wide polarization spectrum with two extremes: M1 or classical activation and M2 or alternative activation. Extracellular vesicles (EVs) secreted from differentially activated macrophages have been shown to have diverse functions, which are primarily attributed to their microRNA cargos. The role of protein cargos in these EVs remains largely unexplored. Therefore, in this study, we focused on the protein cargos in macrophage-derived EVs.

Results Naïve murine bone marrow-derived …

Sprouting Alters Metabolite And Peptide Contents In The Gastrointestinal Digest Of Soybean And Enhances In-Vitro Anti-Inflammatory Activity, Emerson Nolasco, Inga Krassovskaya, Kelvin Hong, Kali Hansen, Sophie Alvarez, Toshihiro Obata, Kaustav Majumder

Department of Nutrition and Health Sciences: Faculty Publications

Sprouting of soybeans can enhance the release of health-beneficial bioactive compounds, especially peptides, and metabolites, while gastrointestinal (GI) digestion alters their biotransformation and bioaccessibility. The present study aimed to evaluate the effect of soybean sprouting and GI digestion in modulating its anti-inflammatory activity. Soybeans were soaked in water overnight (Day 0) and sprouted for two and four days, subjected to simulated GI digestion, and human intestinal epithelial cells (Caco-2) were pretreated (2 h) with soybean sprout digest (SSD: 1000 μg/mL) before inflammation induction with IL-1β. Pre-treatment with Day 4 SSD specifically reduced the secretion of cytokine IL-8 by 19.5%. Sprouting …

Protein Enriched Bread Using Spent Wine Yeast, Zachary Christman

Applied Science Program: Theses

Yeast is a common byproduct of wine production. Wine yeast may be used as a food source. It does not contain bitter and astringent compounds such as those present in spent yeast from making beer The use of nutritional yeast and yeast extract for protein enrichment of bread are presented in this article.

Antibiotic-Induced Gut Dysbiosis And Cognitive, Emotional, And Behavioral Changes In Rodents: A Systematic Review And Meta-Analysis, Shivdeep S. Hayer, Soonjo Hwang, Jonathan B. Clayton

Department of Nutrition and Health Sciences: Faculty Publications

There are previous epidemiological studies reporting associations between antibiotic use and psychiatric symptoms. Antibiotic-induced gut dysbiosis and alteration of microbiota-gut-brain axis communication has been proposed to play a role in this association. In this systematic review and meta-analysis, we reviewed published articles that have presented results on changes in cognition, emotion, and behavior in rodents (rats and mice) after antibiotic-induced gut dysbiosis. We searched three databases—PubMed, Web of Science, and SCOPUS to identify such articles using dedicated search strings and extracted data from 48 articles. Increase in anxiety and depression-like behavior was reported in 32.7 and 40.7 percent of the …

Resistant Potato Starch Supplementation Reduces Serum Histamine Levels In Healthy Adults With Links To Attenuated Intestinal Permeability, Jason R. Bush, Jun Han, Edward C. Deehan, Scott V. Harding, Madhura Maiya, Joshua Baisley, David Schibli, David R. Goodlett

Department of Nutrition and Health Sciences: Faculty Publications

Histamine from our diet or gut microbes can trigger gastrointestinal disturbances, and resistant potato starch (RPS) has previously been shown to alleviate these symptoms while increasing levels of health-associated bacteria such as Akkermansia through unknown mechanisms. Post hoc exploratory metabolomic analysis of serum amino acid, amine, and carnitine metabolites in participants consuming 3.5 g/day RPS or placebo (n = 48) was performed using liquid chromatography-mass spectrometry to determine whether RPS positively influences histamine metabolism and related parameters. Histamine levels were significantly reduced by RPS treatment, but histamine-degrading enzyme products were unaffected by RPS. RPS also reduced histamine-secreting Haemophilus and Lactobacillus …

Fatiguing Joint Angle Does Not Influence Torque And Neuromuscular Responses Following Sustained, Isometric Forearm Flexion Tasks Anchored To Perceptual Intensity In Men, Dolores G. Ortega, Terry J. Housh, Robert Smith, Jocelyn E. Arnett, Tyler J. Neltner, John Paul V. Anders, Richard J. Schmidt, Glen O. Johnson

Department of Nutrition and Health Sciences: Faculty Publications

This study examined the effects of joint angle (JA) on maximal voluntary isometric contraction (MVIC) and neuromuscular responses following fatiguing tasks anchored to RPE. Nine men (mean ± SD: age = 20.7 ± 1.2 yrs) performed forearm flexion MVICs at elbow JAs of 75^o and 125^o before and after sustained, isometric forearm flexion tasks to failure at fatiguing joint angles (FJA) of 75^o and 125^o anchored to RPE = 8. The amplitude and frequency of the electromyographic and mechanomyographic signals were recorded. Neuromuscular efficiency was calculated by dividing normalized torque by normalized electromyographic amplitude. A dependent …

Auricularia Auricula Polysaccharides Attenuate Obesity In Mice Through Gut Commensal Papillibacter Cinnamivorans, Xin Zong, Hao Zhang, Luoyi Zhu, Edward C. Deehan, Jie Fu, Yizhen Wang, Mingliang Jin

Department of Nutrition and Health Sciences: Faculty Publications

Introduction: Auricularia auricula is a well-known traditional edible and medical fungus with high nutritional and pharmacological values, as well as metabolic and immunoregulatory properties. Nondigestible fermentable polysaccharides are identified as primary bioactive constituents of Auricularia auricula extracts. However, the exact mechanisms underlying the effects of Auricularia auricula polysaccharides (AAP) on obesity and related metabolic endpoints, including the role of the gut microbiota, remain insufficiently understood.

Methods: The effects of AAP on obesity were assessed within high-fat diet (HFD)-based mice through obesity trait analysis and metabolomic profiling. To determine the mechanistic role of the gut microbiota in observed anti-obesogenic …

Performance Fatigability And Neuromuscular Responses Are Not Joint Angle Specific Following A Sustained Isometric Forearm Flexion Task Anchored To A High Perceptual Intensity In Women, Jocelyn E. Arnett, Robert W. Smith, Tyler J. Neltner, John Paul V. Anders, Dolores G. Ortega, Terry J. Housh, Richard J. Schmidt, Glen O. Johnson

Department of Nutrition and Health Sciences: Faculty Publications

Objectives: To examine the effects of joint angle (JA) on maximal voluntary isometric contractions (MVIC) and neuromuscular responses following a sustained, isometric forearm flexion task anchored to a rating of perceived exertion (RPE) of 8 (RPE=8). Methods: Nine women (age: 20.7±2.9 yrs; height: 168.8±7.2 cm; body mass: 66.3±6.8 kg) performed 2,3s forearm flexion MVICs at JAs of 75°, 100°, and 125° prior to and following a sustained, isometric forearm flexion task anchored to RPE=8 to task failure (torque reduced to zero) at JA100. Electromyographic (EMG) and mechanomyographic (MMG) signals were recorded from the biceps brachii. Results: The …

Homeobox Transcription Factor Hbxa Influences Expression Of Over One Thousand Genes In The Model Fungus Aspergillus Nidulans, Sandesh S. Pandit, Jinfang Zheng, Yanbin Yin, Sophie Lorber, Olivier Puel, Sourabh Dhingra, Eduardo A. Espeso, Ana M. Calvo

Department of Nutrition and Health Sciences: Faculty Publications

In fungi, conserved homeobox-domain proteins are transcriptional regulators governing development. In Aspergillus species, several homeobox-domain transcription factor genes have been identified, among them, hbxA/hbx1. For instance, in the opportunistic human pathogen Aspergillus fumigatus, hbxA is involved in conidial production and germination, as well as virulence and secondary metabolism, including production of fumigaclavines, fumiquinazolines, and chaetominine. In the agriculturally important fungus Aspergillus flavus, disruption of hbx1 results in fluffy aconidial colonies unable to produce sclerotia. hbx1 also regulates production of aflatoxins, cyclopiazonic acid and aflatrem. Furthermore, transcriptome studies revealed that hbx1 has a broad effect on the A. flavus …

Sesame Eliciting And Safe Doses In A Large Sesame Allergic Population, Liat Nachshon, Joost Westerhout, W. Marty Blom, Benjamin Remington, Michael B. Levy, Michael R. Goldberg, Naama Epstein-Rigbi, Yitzhak Katz, Arnon Elizur

Department of Nutrition and Health Sciences: Faculty Publications

Background: Sesame is a significant food allergen causing severe and even fatal reactions. Given its increasing prevalence in western diet, sesame is listed as an allergenic food requiring labeling in the United States and EU. However, data on the population reaction doses to sesame are limited.

Methods: All sesame oral food challenges (OFCs), performed either for diagnosis or for threshold identification before the beginning of sesame oral immunotherapy (OIT) between November 2011 and July 2021 in Shamir medical center were analyzed for reaction threshold distribution. Safe-dose challenges with 90–120 min intervals were also analyzed.

Results: Two hundred …

Assessment Of The Immune Response In Patients With Insulin Resistance, Obesity, And Diabetes To Covid-19 Vaccination, Jędrzej Warpechowski, Paula Leszczyńska, Dominika Juchnicka, Adam Olichwier, Łukasz Szczerbiński, Adam Jacek Krętowski

Department of Nutrition and Health Sciences: Faculty Publications

The SARS-CoV-19 pandemic overwhelmed multiple healthcare systems across the world. Patients with underlying medical conditions such as obesity or diabetes were particularly vulnerable, had more severe symptoms, and were more frequently hospitalized. To date, there have been many studies on the severity of SARS-CoV-2 in patients with metabolic disorders, but data on the efficiency of vaccines against COVID-19 are still limited. This paper aims to provide a comprehensive overview of the effectiveness of COVID-19 vaccines in individuals with diabetes, insulin resistance, and obesity. A comparison is made between the immune response after vaccination in patients with and without metabolic comorbidities. …

Studies Of The Role Of Mtorc1 In Modulating Intestinal Epithelial Barrier Function, Isaac Adediji

Department of Nutrition and Health Sciences: Dissertations, Theses, and Student Research

Mechanistic target of rapamycin complex 1 (mTORC1) signaling impacts intestinal inflammation by modulating the production of cytokines in both intestinal epithelial cells and macrophages. Recent evidence revealed that THP-1-derived macrophages with elevated mTORC1 activity (THP-1shTSC2 macrophages), exhibited increased proinflammatory cytokine production when stimulated with lipopolysaccharide (LPS) compared to counterpart macrophages with repressed or baseline mTORC1 activity. Furthermore, it has been shown that mTORC1 governs intestinal barrier function as evidenced by elevated transepithelial electrical resistance (TEER) and para/transcellular permeability in Raptor-depleted Caco-2 cells (cells with repressed mTORC1 activity) compared to Caco-2 cells with elevated or baseline mTORC1 activity. The present study …

Literature Review—Transthoracic Echocardiography, Computed Tomography Angiography, And Their Value In Clinical Decision Making And Outcome Predictions In Patients With Covid-19 Associated Cardiovascular Complications, Jędrzej Warpechowski, Adam Olichwier, Aleksandra Golonko, Marcin Warpechowski, Robert Milewski

Department of Nutrition and Health Sciences: Faculty Publications

The sudden outbreak of the COVID-19 pandemic posed a great threat to the world’s healthcare systems. It resulted in the development of new methods and algorithms for the diagnosis and treatment of both COVID-19 and its complications. Diagnostic imaging played a crucial role in both cases. Among the most widely used examinations are transthoracic echocardiography (TTE) and computed tomography angiography (CTA). Cardiovascular complications in COVID-19 are frequently associated with a severe inflammatory response, which results in acute respiratory failure, further leading to severe complications of the cardiovascular system. Our review aims to discuss the value of TTE and CTA in …

Diet-Microbiome-Immune Interplay In Multiple Sclerosis: Understanding The Impact Of Phytoestrogen Metabolizing Gut Bacteria, Peter C. Lehman, Sudeep Ghimire, Jeffrey D. Price, Amanda E. Ramer-Tait, Ashutosh K. Mangalam

Department of Nutrition and Health Sciences: Faculty Publications

Multiple sclerosis (MS) is a chronic and progressive autoimmune disease of the central nervous system (CNS), with both genetic and environmental factors contributing to the pathobiology of the disease. Although HLA genes have emerged as the strongest genetic factor linked to MS, consensus on the environmental risk factors is lacking. Recently, the gut microbiota has garnered increasing attention as a potential environmental factor in MS, as mounting evidence suggests that individuals with MS exhibit microbial dysbiosis (changes in the gut microbiome). Thus, there has been a strong emphasis on understanding the role of the gut microbiome in the pathobiology of …

Curated And Harmonized Gut Microbiome 16s Rrna Amplicon Data From Dietary Fiber Intervention Studies In Humans, Cynthia I. Rodriguez, Ali Keshavarzian, Bruce R. Hamaker, Feitong Liu, Genelle R. Lunken, Heather Rasmussen, Hongwei Zhou, Julien Tap, Kelly S. Swanson, Maria Ukhanova, Marion Leclerc, Martin Gotteland, Paola Navarrete, Petia Kovatcheva-Datchary, Wendy J. Dahl, Jennifer B. H. Martiny

Department of Nutrition and Health Sciences: Faculty Publications

Next generation amplicon sequencing has created a plethora of data from human microbiomes. The accessibility to this scientific data and its corresponding metadata is important for its reuse, to allow for new discoveries, verification of published results, and serving as path for reproducibility. Dietary fiber consumption has been associated with a variety of health benefits that are thought to be mediated by gut microbiota. To enable direct comparisons of the response of the gut microbiome to fiber, we obtained 16S rRNA sequencing data and its corresponding metadata from 11 fiber intervention studies for a total of 2,368 samples. We provide …

Home-Site Advantage For Host Species–Specific Gut Microbiota, Daniel D. Sprockett, Jeff Price, Anthony Juritsch, Robert J. Schmaltz, Madalena V. F. Real, Samantha L. Goldman, Michael Sheehan, Amanda E. Ramer-Tait, Andrew H. Moeller

Department of Nutrition and Health Sciences: Faculty Publications

Mammalian species harbor compositionally distinct gut microbial communities, but the mechanisms that maintain specificity of symbionts to host species remain unclear. Here, we show that natural selection within house mice (Mus musculus domesticus) drives deterministic assembly of the house-mouse gut microbiota from mixtures of native and non-native microbiotas. Competing microbiotas from wild-derived lines of house mice and other mouse species (Mus and Peromyscus spp.) within germ-free wild-type (WT) and Rag1-knockout (Rag1^−/−) house mice revealed widespread fitness advantages for native gut bacteria. Native bacterial lineages significantly outcompeted non-native lineages in both WT and Rag1 …

Genome Mining For Anti-Crispr Operons Using Machine Learning, Bowen Yang, Minal Khatri, Jinfang Zheng, Jitender S. Deogun, Yanbin Yin

Department of Nutrition and Health Sciences: Faculty Publications

Motivation: Encoded by (pro-)viruses, anti-CRISPR (Acr) proteins inhibit the CRISPR-Cas immune system of their prokaryotic hosts. As a result, Acr proteins can be employed to develop more controllable CRISPR-Cas genome editing tools. Recent studies revealed that known acr genes often coexist with other acr genes and with phage structural genes within the same operon. For example, we found that 47 of 98 known acr genes (or their homologs) co-exist in the same operons. None of the current Acr prediction tools have considered this important genomic context feature. We have developed a new software tool AOminer to facilitate the improved …