Source: UNIVERSITY OF NEBRASKA submitted to NRP
MILK EXOSOME-DRIVEN EVOLUTION OF ANTIBIOTIC-RESISTANT GUT PATHOGENS
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
Reporting Frequency
Annual
Accession No.
1021942
Grant No.
2020-67017-30834
Cumulative Award Amt.
$500,000.00
Proposal No.
2019-07758
Multistate No.
(N/A)
Project Start Date
Mar 15, 2020
Project End Date
Mar 14, 2025
Grant Year
2020
Program Code
[A1343]- Food and Human Health
Recipient Organization
UNIVERSITY OF NEBRASKA
(N/A)
LINCOLN,NE 68583
Performing Department
Nutrition and Health Sciences
Non Technical Summary
Exosomes are natural nanoparticles that are abundant in milk. Antibiotics-resistant Clostridiodes (Clostridium) difficile and Enterobacter faecalis are major causes of gastrointestinal disease in the USA. This research studies whether dietary depletion of milk (milk exosomes) selects for mutants of Clostridiodes (Clostridium) difficile and Enterobacter faecalis that are more virulent than Clostridiodes (Clostridium) difficile and Enterobacter faecalis living in a milk exosome-sufficient environment (gut).
Animal Health Component
30%
Research Effort Categories
Basic
70%
Applied
30%
Developmental
0%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
72434501010100%
Knowledge Area
724 - Healthy Lifestyle;

Subject Of Investigation
3450 - Milk;

Field Of Science
1010 - Nutrition and metabolism;
Goals / Objectives
Objective 1. Assess the selection of polymorphisms in C. difficile and vancomycin-resistant E. faecalis in milk exosome-defined cultures. This objective tests the hypothesis that the presence of milk exosomes in culture will select for genetic polymorphisms that may enhance or diminish virulence-associated phenotypes that can be measured in vitro compared to bacteria prior to passaging (reference genome).Objective 2. Assess whether milk exosomes cause changes in the host microbiome that alter the colonization of mice with C. difficile and E. faecalis not selected in exosome cultures. This objective tests the hypothesis that feeding milk exosome and RNA-depleted (ERD) diets and milk exosome and RNA-sufficient (ERS) diets causes changes in microbial communities in the murine gut that alter the susceptibility to challenges with pathogens.Objective 3. Assess the pathogenicity of in vitro-selected polymorphisms in mice fed a regular AIN-93G diet. This objective tests the hypothesis that C. difficile and E. faecalis selected in milk exosome-free (E-Minus) cultures cause disease phenotypes that differ in severity compared to phenotypes caused by C. difficile and E. faecalis selected in milk exosome-supplemented (E-Plus) cultures.
Project Methods
Objective 1Exosome-defined cultures. C. difficile and E. faecalis will be serially passaged under anaerobic conditions at 37°C in defined minimal medium appropriate for growth (C. difficile defined medium or Enterococcus simplified defined medium) for 14 (C. difficile) or seven days (E. faecalis). We chose seven days for E. faecalis because that time frame was sufficient to select for polymorphisms and mutations in preliminary studies. Because C. difficile grows more slowly than E. faecalis, we selected a time frame that represented the equivalent number of generations (~50). The amount of exosomes added to E-Plus media will be the equivalent of exosomes from 0.5 L of bovine milk dispersed in the total GI water in a human adult, adjusted by murine body weight and GI water (i.e., we will use a nutritionally relevant dose of 2.1x1010 exosomes/mL). Fresh exosomes or solvent will be added to cultures daily under anaerobic conditions. Three independent cultures of each strain will be screened in E-Minus and E-Plus cultures. At the end of serial passage, cells will be serially diluted, and aliquots will be spread on Brain Heart Infusion (BHI) medium to identify isolated colonies. Ten isolates per culture of each strain will be saved for further testing. Following passage, strains will be verified as C. difficile 2015 or E. faecalis BAA-2365 through PCR.Assessment of potential pathogenicity through in vitro screening. We have delineated the following strategy, which is based on pathogenicity, for prioritizing polymorphisms. High throughput assays will be used to screen through the 120 strains (three independent cultures x two culture conditions x two pathogens x 10 isolates/culture) identified at the end of serial passaging to identify strains with behavior changes that likely correlate with increased pathogenesis in vivo. For C. difficile isolates, growth rate, toxin production, sporulation, biofilm formation, and competitive fitness compared to the parental strain will be evaluated as previously described to identify isolates with newly acquired traits that likely correlate with changes in virulence in vivo. For E. faecalis, growth rate, biofilm formation, gelatinase, b-hemolysis, and competitive fitness compared to the parental strain will be evaluated as previously described. Changes in minimal inhibitory concentrations to a panel of clinically-relevant antibiotics will also be evaluated. Isolates exhibiting the largest changes relative to baseline will be selected for whole genome sequencing (see Expected results below).Identification of polymorphisms and mutations. Two C. difficile and E. faecalis isolates per independent culture will be grown in BHI and pelleted by centrifugation (20,000 g, five minutes). DNA will be extracted with a DNEasy Blood and Tissue Kit (Qiagen). Genome sequencing, assembly, and variant calling relative to the baseline genomes prior to serial passage will be completed by MiGS (University of Pittsburgh).Objective 2Mice. To capture the effects of sex and age, we will conduct studies in male and female C57BL/6 mice (Jackson Labs, strain 000664) at ages 7 and 15 weeks.Diets. The ERS and ERD diets are based on the AIN-93G diet. The content of all macronutrients and micronutrients is identical in ERS, ERD, and AIN-93G except for the content of milk exosomes and their cargos. AIN-93G was developed in 1993 with the goal of achieving optimal growth in mice. However, the importance of milk exosomes was not recognized until 2014. In this study, we will use AIN-93G as a control and ERS and ERD as milk exosome-defined treatments. All diets will be used in pelleted form.In the section "Preliminary Studies, Objective 2," we discussed the preparation of ERS and ERD diets, loss of milk exosomes (20% loss) and exosome bioavailability (>50% loss), and loss of exosome cargos (>98% loss) in ERD compared to ERS. Note that both ERD and ERS diets provide the equivalent of 0.5 L milk in a human adult per day, which is a nutritionally relevant dose, adjusted by the body weight of mice. In a previous study, ERS and ERD did not affect food and water intake and frequency, physical activity, respiratory exchange ratio, body weight, and variables of clinical chemistry (serum enzymes and electrolytes).Bacteria. As in Objective 1, we will use clinical isolates of C. difficile and E. faecalis. C. difficile spores will be isolated from stationary phase cultures as previously described1, and spore titers will be determined by selective plating. E. faecalis cells will be grown in BHI and collected by centrifugation (20,000 g, two minutes) one hour after entry into the stationary phase. Cells will be washed twice with phosphate buffered saline and stored at -80°C93. CFU/ml will be determined by selective plating.Experimental design. A 3 x 2 x 2 factorial design will be used (diet x bacterial challenge x age). Selection bias will be avoided by assigning each mouse a number and randomly assigning numbers to treatment groups94. Feeding will be initiated at age three weeks and continued for four or 12 weeks, which was sufficient to elicit changes in microbial communities in preliminary studies. Antibiotic-treated mice will be challenged with 104 spores from C. difficile or 1010 E. faecalis that were not selected in E-Plus and E-Minus media by oral gavage. Cage effects will be minimized by pulling mice from groups housed in separate cages. The following variables will be assessed:Changes in body massC. difficile and E. faecalis loadC. difficile toxin levelsFood and water consumption.Mucosal cytokinesHistopathologyFeces (diarrhea)SurvivalMicrobial communitiesObjective 3Mice. To capture the effects of sex and age, we will conduct studies in male and female C57BL/6 mice (Jackson Labs, strain 000664) at ages 7 and 15 weeks.Diets. Mice will be fed the AIN-93G diet.Exosomes. Our protocols for isolating and authenticating milk exosomes are described in preliminary studies. Briefly, exosomes will be isolated from store-bought cow's milk using sequential ultracentrifugation. We will authenticate our exosome preparations following the guidelines by the International Society for Extracellular Vesicles as previously described. Preparations that show signs of exosome aggregation (by transmission electron microscopy) or contamination with fat globules, lipoproteins, microvesicles, or casein micelles (by immunoblot analysis) will be discarded or further purified using size exclusion chromatography, iodixanol gradient centrifugation, or affinity chromatography following protocols endorsed by the extracellular RNA Consortium at the National Institutes of Health and routinely used in our laboratory. Exosomes will be sterile-filtered using a 0.22-µm membrane and stored in phosphate-buffered saline at -80ºC.Bacteria. C. difficile strains with polymorphisms selected during growth in E-Plus and E-Minus defined medium will be grown in the same medium until spore formation is detected by microscopy. Spores then will be prepared as described in Objective 2. Frozen E. faecalis strains with polymorphisms selected during growth in E-Plus and E-Minus will be thawed and grown in the same medium until one hour into the stationary phase. They will be prepared for administration to mice as described in Objective 2.Experimental design. A 2 x 2 x 2 factorial design will be used (in vitro selection x bacterial challenge x age). Randomization of group assignments will be achieved as described in Objective 2. Mice will be fed the AIN-93G diet beginning at age three weeks and will continue the diet for four weeks to establish an equilibrium of gut microbiota. Mice will be challenged with 104 spores from C. difficile or 1010 E. faecalis that were selected in E-Plus and E-Minus media by oral gavage. We will assess the same variables as described in Objective 2.

Progress 03/15/20 to 03/14/25

Outputs
Target Audience:The target audience includes scientists (faculty, postdocs, students) in nutrition and biomedical science, officials form federal agencies, policy makers, dairy industry, journalists, and lay public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project has provided support for two faculty members, Dr. J. Zempleni (PD) and J. Auchtung (Co-PD) and a postdoctoral associate (Dr. Shu Wang). Dr. Zempleni has acquired new knowledge in studies of microbiology. Dr. Auchtung has acquired new knowledge in milk exosomes nutrition. The postdoctoral associate was new to microbiology and has acquired expertise in this area. How have the results been disseminated to communities of interest?The new knowledge generated in this project has been disseminated to target audiences through publications in peer-reviewed journals, invited seminars, and presentations at local, national, and international conferences (see Products and Other Products). What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Objective 1. We demonstrated that milk exosomes selected a deletion in the phosphotransferase domain in the ptsG gene ("ptsG _indel"). The ptsG gene facilitates glucose transport in bacteria and is implicated in pathogenicity C. difficile. Exosome-selected C. difficile grew faster and produced less toxin than non-selected controls. Findings were corroborated in ptsG and ptsG_indel overexpression studies. C. difficile in milk exosome-containing media grew 15% to 20% faster than controls cultured in exosome-free media. The production of toxins, tcdA and tcdB, was 60% to 90% lower in the various milk exosome (ME)-containing cultures of C. difficile compared to exosome-free control cultures. We observed that overexpression of ptsG_indel increased growth and reduced toxin production in C. difficile. This observation is consistent with our hypothesis that MEs select for polymorphisms that decrease the pathogenicity of gut pathogens. We discovered that MEs selected a mutation in the DNA binding domain in the catabolite control protein A (ccpA) gene in E. faecalis. The ccpA gene is a transcriptional regulator of carbon catabolite repression and carbon catabolite activation, which ensures optimal energy usage under diverse conditions. Wild-type E. faecalis grew slower with an increased generation time when cultured in ME-free compared to ME-containing media. Conclusion Collectively, we demonstrated that MEs 1) promote the growth of commensal gut pathogens ex vivo and 2) select mutations in genes implicated in carbohydrate metabolism bacterial virulence. Objective 2. Preface The studies depend on feeding ME-defined diets. Briefly, we have developed rodent diets defined by their content of MEs and the RNA content. The diets are based on the AIN-93G formulation. The exosome and RNA-sufficient (ERS) diet contains a nutritionally relevant dose of MEs and RNA cargo (equivalent to 0.5 L milk consumed by an adult), whereas the content of RNA and exosomes is decreased by 8% and up to 99%, respectively, in the exosome and RNA-deficient (ERD) diet. Al other content is identical in ERS and ERD diets. Recap previous reporting periods In Years 1 and 2, we fed C57BL/6 mice ERD and ERS diets for four weeks starting at age 3.5 to 4.5 weeks and challenged the mice with an oral dose of 105 spores from C. difficile. Survival of mice fed the ERD diet decreased by approximately 50% compared to mice fed the ERS diet (P < 0.05). Consistent with this observation, the median clinical sickness scores (B. Fehlhaber et al, Sci. Rep. 2019; 9: 5919; PMC6459866).in mice fed an ERD diet were 3-fold higher than mice fed the ERS (P < 0.01). We assessed bacterial communities in mice fed ERD and ERS diets with C. difficile. challenge) by using 16S rRNA sequencing. We observed significant changes in a small number of taxa between treatment groups on day 3 followingC. difficilechallenge. ERS feeding resulted in an increase ofLachnospiraceae, Bacteroides(5operational taxonomic units, OTUs) andAlistipes(2OTUs), whereas ERD resulted in an increase ofAkkermansia,Escherichia/Shigella,Enterococcaceae, andClostridiumsensustricto. Since Escherichia/ShigellaandEnterococcaceae are associated with increased disease severity, we concluded that the protective effects of ERS diet on the host response might be due to the selection protective taxa and decrease of pathobionts. We observed that myeloperoxidase activity, a marker of neutrophil infiltration was significantly higher in mice fed an ERD diet on day 7 of infection compared to mice fed an ERS diet, pointing to higher levels of inflammation in the absence of milk exosomes. We conducted additional feeding studies and challenged the mice with C.difficile. Seven days post C. difficile, the myeloperoxidase (MPO) activity, which was used to assess the neutrophil/granulocyte infiltration, was higher in cecum and colon from ERD-fed mice than that from ERS-fed mice; IL-17b was also higher in the colon from ERD-fed mice compared to ERS-fed mice. This reporting period (no-cost extension) We investigated the effects of dietary bovine MEs on bacterial translocation and immune responses in a mouse model of Enterococcus faecalis infection. Mice fed a ME-sufficient diet for 4 weeks and treated with cyclophosphamide and a combination of antibiotics (metronidazole, kanamycin and vancomycin). Mice were challenged with 1) wild-type (reference strain), 2) ME-selected, or 3) vehicle (solvent, PBS)-selected E. faecalis strains. Quantitative qPCR analysis using universal 16S rRNA primers revealed no significant differences in bacterial translocation to the spleen among the groups. However, a 2.3-fold reduction in bacterial levels in the liver was observed for the ME-selected E. faecalis strain compared to the wild-type strain (p = 0.0445). Furthermore, we assessed inflammatory responses by quantifying four key markers (TNF-alpha, IL-10, IL-1beta, and MIP-2) associated with E. faecalis infections and mouse immune responses in the cecum. No significant differences in the levels of these markers were detected between treatment groups. These findings suggest that while ME selection may have a minor impact on bacterial localization to the liver, it does not significantly influence systemic bacterial translocation or local inflammatory responses in this model. Conclusion Data are consistent with our proposal's hypotheses that MEs 1) alter bacterial communities in the gut, and 2) enhance the colonization with protective taxa, and 3) have a beneficial effect on hosts challenged with C. difficile, whereas beneficial effects are comparably minor, and limited to reduced bacterial translocation, in E. faecalis. Objective 3. Please see Objective 3. In addition to ERS and ERD diets, we fed mice with AIN-93G. The mice were challenged with C. difficile and pathogenicity was assessed by monitoring the mortality, weight loss over the time, and measuring the C.difficile CFU and toxin activity present in the fecal samples. Results were inconclusive and the feeding study was repeated in Year 3 to increase the sample size. We demonstrated that the minor content of lactose in experimental diets is not a confounder in studies of mice (which are lactose intolerant; see the manuscript by Sukreet et al. in Products). We fed C57/BL6 mice on ERS and ERD diets and challenged them with C. difficile that were selected in the absence or presence of MEs. We observed that when mice fed the ERS diet, mortality was lower in mice challenged with C. difficile grown in the presence of MEs compared to mice C. difficile grown in the absence of MEs (10% versus 22% seven days after the challenge). Weight loss was also lower in mice challenged with C. difficile selected by MEs than in C. difficile not selected by MEs (3.5% versus 11.4% six days after challenge). Conclusion Collectively, our studies to date are consistent with our proposal's hypothesis that a ME-depleted diet (ERD) increases the susceptibility of mice to challenge with C. difficile. The AIN-93G diet did not increase the susceptibility. We speculate that casein in AIN-93G provided contains MEs. Casein is not present in the ERD diet. Beneficial effects are comparably minor, and limited to reduced bacterial translocation, in E. faecalis.

Publications

  • Type: Peer Reviewed Journal Articles Status: Published Year Published: 2025 Citation: Zhou F, Mumtaz PT, Dogan H, Madadjim R, Cui J, Zempleni J. Divergence of gut bacteria through the selection of genomic variants implicated in the metabolism of sugars, amino acids, and purines by small extracellular vesicles in milk. Gut Microbes 17 (1):2449704, 2025
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Setayesh L, Zempleni J. Preserving milk exosome integrity during storage: strategies for minimizing loss. University of Nebraska, Student Research Days, Lincoln, NE, March 27, 2024
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Zempleni J. Milk exosome-driven evolution of antibiotic-resistant gut pathogens. NIFA grantee meeting, Human Health Program (A1343), Purdue University, Lafayette, IN, May 23, 2024
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Zempleni J. Milk exosomes. USDA W-5002 Multistate Group meeting, UC-Davis, CA, May 29, 2024 [talk]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Setayesh L, Zempleni J. Minimizing the loss of extracellular vesicles in human milk. Nutrition 2024 Conference, American Society for Nutrition; Chicago, IL, 6/29  7/2, 2024
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Zaman BW B, Madajim R, Cui J, Zempleni J. Effects of Dairy Consumption on Gene Expression in Gut Bacteria in Adults. Nutrition 2024 Conference, American Society for Nutrition; Chicago, IL, 6/29  7/2, 2024
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Zaman Wahid B, Madadjim R, Cui J, Zempleni J. Effects of dairy consumption on gene expression in gut bacteria in adults. University of Nebraska, University of Nebraska-Lincoln, NPOD 10th Annual Fall Research Symposium, October 8, 2024 [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Mumtaz PT, Zempleni J. Bifidobacterium infantis extracellular vesicles: composition and potential to modulate host biological processes via cross-kingdom communication. University of Nebraska-Lincoln, NPOD 10th Annual Fall Research Symposium, October 8, 2024
  • Type: Conference Papers and Presentations Status: Published Year Published: 2025 Citation: Zempleni J. Milk exosomes in nutrition and drug delivery. Presentation to the Manitoba Interdisciplinary Lactation Centre. February 12, 2025 [invited oral presentation; zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Zaman Wahid B, Madadjim R, Cui J, Zempleni J. Effects of dairy consumption on gene expression in gut bacteria in adults. UNL Research Days, University of Nebraska-Lincoln; Lincoln, NE, March 27, 2024


Progress 03/15/23 to 03/14/24

Outputs
Target Audience:The target audience includes scientists (faculty, postdocs, students) in nutrition, biomedical science, policy makers, dairy industry, journalists and lay public. Changes/Problems:The postoc conducting the hands-on work unexpectedly left the lab. WE had to replace her with another postdoc who had to undergo some training. What opportunities for training and professional development has the project provided?The project provides support for two faculty, Drs. J. Zempleni (PD) and J. Auchtung (co-PD), a postdoctoral associate (Dr. S. Wang, replaced with Dr. Qamar Taban in Year 4) and a research technologist. Dr. Zempleni has acquired new knowledge in studies of microbiology, whereas Dr. Auchtung has acquired new knowledge in nutrition research, dairy and milk exosomes. The postdoctoral associate was new to both microbiology and milk exosome research and has acquired expertise in both areas. The technologist was new to milk exosome research and has acquired technical skills in that area. The postdoctoral associate present and Dr. Zempleni findings from this study at scientific conferences though invited seminars and presentations at scientific conferences (see Products). How have the results been disseminated to communities of interest?Results have been disseminated through invited seminars and presentations at scientific conferences, and websites and blogs (see Products and Other Products). What do you plan to do during the next reporting period to accomplish the goals?1. Complete the bioinformatics analysis of RNA-sequencing analysis data to assess ME-dependent gene expression pathways in bacteria. 2. Assess whether a modified stud protocol leads to a stronger phenotype of mutations in E. faecalis than what we have observed in studies completed to date. 3. Manuscript submissions.

Impacts
What was accomplished under these goals? Objective 1. Recap previous reporting periods Previously, we reported that milk exosomes selected a deletion in the phosphotransferase (PTS_EIIA_1) domain in the ptsG gene ("ptsG _indel"). The ptsG gene facilitates glucose transport in bacteria and is implicated in pathogenicity C. difficile. Exosome-selected C. difficile grew faster and produced less toxin than non-selected controls. C. difficile in milk exosome-containing media grew 15% to 20% faster than controls cultured in exosome-free media. The production of toxins, tcdA and tcdB, was 60% to 90% lower in the various milk exosome (ME)-containing cultures of C. difficile compared to exosome-free control cultures. Toxin production was assessed by using real-time PCR and by using cytotoxic effects in Vero cells (A. Valdiviesco-Garcia et al., 1993; 59: 1981-1983). We have developed strains of C. difficile that overexpress wild-type ptsG or ptsG_indel, and we are working towards developing ptsG knockout C. difficile. Using these strains, we started interrogating effects of ptsG overexpression on growth and toxin production. We observed that overexpression of ptsG_indel increased growth and reduced toxin production in C. difficile. This observation is consistent with our hypothesis that MEs select for polymorphisms that decrease the pathogenicity of gut pathogens. This reporting period In this reporting period we discovered that MEs selected a mutation in the DNA binding domain in the catabolite control protein A (ccpA) gene in E. faecalis. The ccpA gene is a transcriptional regulator of carbon catabolite repression and carbon catabolite activation, which ensures optimal energy usage under diverse conditions. Wild-type E. faecalis grew slower with an increased generation time when cultured in ME-free compared to ME-containing media. When E. faecalis was cultured in ME-defined media prior to transfer and continued culturing in minimal media, the polymorphisms and mutations selected in ME-containing media led to a slower growth in minimal media compared to polymorphisms and mutations selected in ME-free media We observed that E. faecalis that were cultured in ME-supplemented media grew faster and had a shortened generation time compared with E. faecalis that were cultured in ME-free media. We further tested the biofilm production by these E. faecalis after selection. (Biofilm production is associated with virulence and antimicrobial resistance.) We are in the process of completing the bioinformatics analysis of RNA-sequencing analysis data to assess ME-dependent gene expression pathways in bacteria. Interim conclusion Collectively, our studies to date are consistent with our proposal's hypotheses that MEs 1) select polymorphisms and mutations in gut bacteria, and 2) ME-driven selection decreases the virulence of gut pathogens. Objective 2. Preface The studies depend on feeding ME-defined diets. Briefly, we have developed [and published (Sukreet et al, se Products)] rodent diets defined by their content of MEs and the RNA content. The diets a re based on the AIN-93G formulation. The exosome and RNA-sufficient (ERS) diet contains a nutritionally relevant dose of MEs and RNA cargo (equivalent to 0.5 L milk consumed by an adult), whereas the the content of RNA and exosomes is decreased by 8% and up to 99%, respectively, in the exosome and RNA-deficient (ERD) diet. Al other content is identical in ERS and ERD diets. Recap previous reporting periods In Years 1 and 2, we fed C57BL/6 mice ERD and ERS diets for four weeks starting at age 3.5 to 4.5 weeks and challenged the mice with an oral dose of 105 spores from C. difficile. Survival of mice fed the ERD diet decreased by approximately 50% compared to mice fed the ERS diet (P < 0.05). Consistent with this observation, the median clinical sickness scores (B. Fehlhaber et al, Sci. Rep. 2019; 9: 5919; PMC6459866).in mice fed an ERD diet were 3-fold higher than mice fed the ERS (P < 0.01). We assessed bacterial communities in mice fed ERD and ERS diets with C. difficile. challenge) by using 16S rRNA sequencing. We observed significant changes in a small number of taxa between treatment groups on day 3 followingC. difficilechallenge. ERS feeding resulted in an increase ofLachnospiraceae, Bacteroides(5operational taxonomic units, OTUs) andAlistipes(2OTUs), whereas ERD resulted in an increase ofAkkermansia,Escherichia/Shigella,Enterococcaceae, andClostridiumsensustricto. Since Escherichia/ShigellaandEnterococcaceae are associated with increased disease severity, we concluded that the protective effects of ERS diet on the host response might be due to the selection protective taxa and decrease of pathobionts. We observed that myeloperoxidase activity, a marker of neutrophil infiltration was significantly higher in mice fed an ERD diet on day 7 of infection compared to mice fed an ERS diet, pointing to higher levels of inflammation in the absence of milk exosomes. We conducted additional feeding studies and challenged the mice with C.difficile. Seven days post C. difficile, the myeloperoxidase (MPO) activity, which was used to assess the neutrophil/granulocyte infiltration, was higher in cecum and colon from ERD-fed mice than that from ERS-fed mice; IL-17b was also higher in the colon from ERD-fed mice compared to ERS-fed mice. This reporting period In this reporting period, we fed C57BL/6 mice ERD and ERS diets for four weeks starting at age 3.5 to 4.5 weeks and challenged the mice with an oral dose of 1010 CFU from E. faecalis. E. faecalis colonized in the colon and cecum more efficiently in mice fed ERD diets compared to ERS controls. Symptoms of bacteria translocation to blood, spleen, and liver are seldom seen in both groups. Going forward, we will try to collect these measurements. Interim conclusion Collectively, our studies to date are consistent with our proposal's hypotheses that MEs 1) alter bacterial communities in the gut, and 2) enhance the colonization with protective taxa. Objective 3. Recap previous reporting periods Please see Objective 3. In addition to ERS and ERD diets, we fed mice with AIN-93G. The mice were challenged with C. difficile and pathogenicity was assessed by monitoring the mortality, weight loss over the time, and measuring the C. difficile CFU and toxin activity present in the fecal samples. Results were inconclusive and the feeding study was repeated in Year 3 to increase the sample size. We demonstrated that the minor content of lactose in experimental diets is not a confounder in studies of mice (which are lactose intolerant; see the manuscript by Sukreet et al. in Products). This reporting period In Year 3, we fed C57/BL6 mice on ERS and ERD diets and challenged them with C. difficile that were selected in the absence or presence of MEs. We observed that when mice fed the ERS diet, mortality was lower in mice challenged with C. difficile grown in the presence of MEs compared to mice C. difficile grown in the absence of MEs (10% versus 22% seven days after the challenge). Weight loss was also lower in mice challenged with C. difficile selected by MEs than in C. difficile not selected by MEs (3.5% versus 11.4% six days after challenge). Effects of mutations on host health were less severe in E. faecalis than C. difficile. In the upcoming final year of the project, we will repeat studies using a modified exosome feeding protocol in mice. Interim conclusion Collectively, our studies to date are consistent with our proposal's hypothesis that a ME-depleted diet (ERD) increases the susceptibility of mice to challenge with C. difficile. The AIN-93G diet did not increase the susceptibility. We speculate that casein in AIN-93G provided contains MEs. Casein is not present in the ERD diet.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Ngu A. and Zempleni J. Genetically modified bovine milk exosomes (BMEs) evade elimination by murine bone marrow-derived macrophages (BMDMs). University of Nebraska, 14th Annual NPOD Research Retreat, April 25, 2023, Lincoln, NE [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Mumtaz PT, Zempleni J. Bifidobacterium infantis extracellular vesicles: cargo content, internalization by human intestinal Caco-2 cells, and bioavailability and distribution in mice. University of Nebraska, NPOD 14th Annual NPOD Spring Retreat, April 25, 2023, Lincoln, NE [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Mumtaz PT, Zempleni J. Bifidobacterium infantis-derived EVs carry a diverse cargo of compounds and are bioavailable in C57BL/6J mice and internalized by human intestinal Caco-2 cells. University of Nebraska, NPOD 14th Annual Research Retreat April 25, 2023 [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Wang S, Auchtung J, Zempleni J. Milk exosomes select mutations that decrease the toxicity of Clostridioides difficile. University of Nebraska, University of Nebraska, NPOD 14th Annual Research Retreat April 25, 2023 [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Setayesh L, Zempleni J. Impact of storage conditions on the quantity and integrity of exosomes and their cargo in human milk. University of Nebraska, NPOD 14th Annual Research Retreat April 25, 2023 [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Zempleni J. Milk exosomes and their relevance in human nutrition and the delivery of therapeutics. Washinton University School of Medicine, St. Louis, MO, May 11, 2023 [talk]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Zempleni J. Divergence of gut bacteria through the selection of genomic variants by small extracellular vesicles in milk. Annual meeting of the International Society for Extracellular Vesicles, Seattle, WA, May 18, 2023 [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Zempleni J. Milk exosomes in Nutrition and drug delivery. USDA W-4002 Multistate Group meeting, Honolulu, HI, May 25, 2023 [talk]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Zempleni J. Milk exosome-driven evolution of antibiotic-resistant gut pathogens. NIFA1343 grantee virtual meeting, July 5, 2023 [talk]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Zempleni J, Zhou F, Dogan H, Madadjim R, Tajamul Mumtaz P, Cui J. Selection of genomic variants i gut bacteria through by small extracellular vesicles in milk: implications for purine metabolism in the host. International Milk Genomics Consortium 2023 Annual Meeting, Cork, Ireland, September 6-8, 2023 [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Setayesh L, Zempleni J. Preserving Milk Exosome Integrity During Storage: Strategies for Minimizing Loss. University of Nebraska, University of Nebraska, NPOD 9th Annual Fall Research Symposium, September 26, 2023 [poster]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Mumtaz P. T and Zempleni J. Exploring Cross-Kingdom Communication with Microbial Messengers: Bifidobacterium infantis EVs' Diverse Cargo, Bioavailability in Mice, and Interaction with Human Intestinal Cells (Caco 2). University of Nebraska, NPOD 9th Annual Research Symposium, September 26, 2023
  • Type: Conference Papers and Presentations Status: Published Year Published: 2023 Citation: Zempleni J. Milk exosomes and their relevance in human nutrition and the delivery of therapeutics. University of Wisconsin-Madison, October 12, 2023 [invited talk]
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Fratantonio D, Munir J, Shu J, Howard K, Baier SR, Cui J, Zempleni. The RNA cargo in small extracellular vesicles from chicken eggs is bioactive in C57BL/6J mice and human peripheral blood mononuclear cells ex vivo. Front Nutr 10:1162679, 2023
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Khanam, A., Ngu A, Zempleni J. Bioavailability of orally administered small extracellular vesicles from bovine milk in C57BL/6J mice. Int J Pharm 639:122974, 2023
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Sukreet S, Braga CP, Adamec J, Cui J, Zempleni J. The absorption of bovine milk small extracellular vesicles depends on Galectin-3 and galactose ligands in human intestinal cells and C57BL/6J mice. Am J Physiol Cell Physiol 325:C1421-1430, 2023
  • Type: Journal Articles Status: Submitted Year Published: 2023 Citation: Wu, D, Shu, J, Braga CP, Cui J, Adamec J, Zempleni J. Bovine mRNAs in small extracellular vesicles from cows milk are bioavailable in mice but translation products are not detectable in reticulocyte lysates and human U937 cells
  • Type: Book Chapters Status: Awaiting Publication Year Published: 2023 Citation: Kuroishi T, Zempleni J. Biotin. In: Modern Nutrition in Health and Disease. Tucker K (editor). Jones & Bartlett Learning, Burlington, MA (in press).
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Munir J, Ngu A, Wang H, Ramirez DMO, Zempleni J. Review: Milk small extracellular vesicles for use in the delivery of therapeutics. Pharm Res 40:909-915, 2023
  • Type: Journal Articles Status: Published Year Published: 2023 Citation: Ngu A,* Munir J,* Zempleni J. Milk-borne small extracellular vesicles: kinetics and mechanisms of transport, distribution, and elimination. Extracell Vesicles Circ Nucleic Acids 4:339-346, 2023
  • Type: Journal Articles Status: Awaiting Publication Year Published: 2023 Citation: Welsh, J, MISEV Consortium [full list of authors on page 42 of the paper]. Minimal information for studies of extracellular vesicles (MISEV2023): from basic to advanced approaches. J Extracell Vesicles


Progress 03/15/22 to 03/14/23

Outputs
Target Audience:The target audience includes scientists (faculty, postdocs, students) in nutrition, biomedical science, policy makers, dairy industry, journalists and lay public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provides support for two faculty, Drs. J. Zempleni (PD) and J. Auchtung (co-PD), a postdoctoral associate (Dr. S. Wang) and a research technologist. Dr. Zempleni has acquired new knowledge in studies of microbiology, whereas Dr. Auchtung has acquired new knowledge in nutrition research, dairy and milk exosomes. The postdoctoral associate was new to both microbiology and milk exosome research and has acquired expertise in both areas. The technologist was new to milk exosome research and has acquired technical skills in that area. The postdoctoral associate present and Dr. Zempleni findings from this study at scientific conferences though invited seminars and presentations at scientific conferences (see Products). How have the results been disseminated to communities of interest?Results have been disseminated through invited seminars and presentations at scientific conferences (see Products). What do you plan to do during the next reporting period to accomplish the goals?1. Challenge mice on ERS, ERD and AIN-93G diets with ptsG knockout C. difficile. 2. Challenge mice on ERS, ERD and AIN-93G diets with selected E. faecalis strains. 3. Complete challenging mice on ERS and ERD diet with E. faecalis. 4. Perform transcriptome analysis on milk exosomes selected and non-selected C. difficile and E. faecalis. 5. Finalize the testing of biofilm production by E. faecalis selected in milk exosome-defined media. 6. Manuscript submissions.

Impacts
What was accomplished under these goals? Objective 1. Recap previous reporting periods Previously, we reported that milk exosomes selected a deletion in the phosphotransferase (PTS_EIIA_1) domain in the ptsG gene ("ptsG _indel"). The ptsG gene facilitates glucose transport in bacteria and is implicated in pathogenicity C. difficile. Exosome-selected C. difficile grew faster and produced less toxin than non-selected controls. C. difficile in milk exosome-containing media grew 15% to 20% faster than controls cultured in exosome-free media. The production of toxins, tcdA and tcdB, was 60% to 90% lower in the various milk exosome (ME)-containing cultures of C. difficile compared to exosome-free control cultures. Toxin production was assessed by using real-time PCR and by using cytotoxic effects in Vero cells (A. Valdiviesco-Garcia et al., 1993; 59: 1981-1983). We have developed strains of C. difficile that overexpress wild-type ptsG or ptsG_indel, and we are working towards developing ptsG knockout C. difficile. Using these strains, we started interrogating effects of ptsG overexpression on growth and toxin production. We observed that overexpression of ptsG_indel increased growth and reduced toxin production in C. difficile. This observation is consistent with our hypothesis that MEs select for polymorphisms that decrease the pathogenicity of gut pathogens. We have selected polymorphisms in vancomycin-resistant E. faecalis cultures in ME-defined cultures, but the variants were not fully characterized. This reporting period In this reporting period we discovered that MEs selected a mutation in the DNA binding domain in the catabolite control protein A (ccpA) gene in E. faecalis. The ccpA gene is a transcriptional regulator of carbon catabolite repression and carbon catabolite activation, which ensures optimal energy usage under diverse conditions. Wild-type E. faecalis grew slower with an increased generation time when cultured in ME-free compared to ME-containing media. When E. faecalis was cultured in ME-defined media prior to transfer and continued culturing in minimal media, the polymorphisms and mutations selected in ME-containing media led to a slower growth in minimal media compared to polymorphisms and mutations selected in ME-free media We observed that E. faecalis that were cultured in ME-supplemented media grew faster and had a shortened generation time compared with E. faecalis that were cultured in ME-free media. We further tested the biofilm production by these E. faecalis after selection. (Biofilm production is associated with virulence and antimicrobial resistance.) Results were inconclusive regarding the effects of ME selection on biofilm production. We will repeat these studies in Year 4. Interim conclusion Collectively, our studies to date are consistent with our proposal's hypotheses that MEs 1) select polymorphisms and mutations in gut bacteria, and 2) ME-driven selection decreases the virulence of gut pathogens. Objective 2. Preface The studies depend on feeding ME-defined diets. Briefly, we have developed [and published (Sukreet et al, se Products)] rodent diets defined by their content of MEs and the RNA content. The diets a re based on the AIN-93G formulation. The exosome and RNA-sufficient (ERS) diet contains a nutritionally relevant dose of MEs and RNA cargo (equivalent to 0.5 L milk consumed by an adult), whereas the the content of RNA and exosomes is decreased by 8% and up to 99%, respectively, in the exosome and RNA-deficient (ERD) diet. Al other content is identical in ERS and ERD diets. Recap previous reporting periods In Years 1 and 2, we fed C57BL/6 mice ERD and ERS diets for four weeks starting at age 3.5 to 4.5 weeks and challenged the mice with an oral dose of 105 spores from C. difficile. Survival of mice fed the ERD diet decreased by approximately 50% compared to mice fed the ERS diet (P < 0.05). Consistent with this observation, the median clinical sickness scores (B. Fehlhaber et al, Sci. Rep. 2019; 9: 5919; PMC6459866).in mice fed an ERD diet were 3-fold higher than mice fed the ERS (P < 0.01). We assessed bacterial communities in mice fed ERD and ERS diets with C. difficile. challenge) by using 16S rRNA sequencing. We observed significant changes in a small number of taxa between treatment groups on day 3 followingC. difficilechallenge. ERS feeding resulted in an increase ofLachnospiraceae, Bacteroides(5operational taxonomic units, OTUs) andAlistipes(2OTUs), whereas ERD resulted in an increase ofAkkermansia,Escherichia/Shigella,Enterococcaceae, andClostridiumsensustricto. Since Escherichia/ShigellaandEnterococcaceae are associated with increased disease severity, we concluded that the protective effects of ERS diet on the host response might be due to the selection protective taxa and decrease of pathobionts. We observed that myeloperoxidase activity, a marker of neutrophil infiltration was significantly higher in mice fed an ERD diet on day 7 of infection compared to mice fed an ERS diet, pointing to higher levels of inflammation in the absence of milk exosomes. We conducted additional feeding studies and challenged the mice with C.difficile. Seven days post C. difficile, the myeloperoxidase (MPO) activity, which was used to assess the neutrophil/granulocyte infiltration, was higher in cecum and colon from ERD-fed mice than that from ERS-fed mice; IL-17b was also higher in the colon from ERD-fed mice compared to ERS-fed mice. This reporting period In this reporting period, we fed C57BL/6 mice ERD and ERS diets for four weeks starting at age 3.5 to 4.5 weeks and challenged the mice with an oral dose of 1010 CFU from E. faecalis. E. faecalis colonized in the colon and cecum more efficiently in mice fed ERD diets compared to ERS controls. Symptoms of bacteria translocation to blood, spleen, and liver are seldom seen in both groups. Going forward, we will try to collect these measurements. Interim conclusion Collectively, our studies to date are consistent with our proposal's hypotheses that MEs 1) alter bacterial communities in the gut, and 2) enhance the colonization with protective taxa. Objective 3. Recap previous reporting periods Please see Objective 3. In addition to ERS and ERD diets, we fed mice with AIN-93G. The mice were challenged with C. difficile and pathogenicity was assessed by monitoring the mortality, weight loss over the time, and measuring the C.difficile CFU and toxin activity present in the fecal samples. Results were inconclusive and the feeding study was repeated in Year 3 to increase the sample size. We demonstrated that the minor content of lactose in experimental diets is not a confounder in studies of mice (which are lactose intolerant; see the manuscript by Sukreet et al. in Products). This reporting period In Year 3, we fed C57/BL6 mice on ERS and ERD diets and challenged them with C. difficile that were selected in the absence or presence of MEs. We observed that when mice fed the ERS diet, mortality was lower in mice challenged with C. difficile grown in the presence of MEs compared to mice C. difficile grown in the absence of MEs (10% versus 22% seven days after the challenge). Weight loss was also lower in mice challenged with C. difficile selected by MEs than in C. difficile not selected by MEs (3.5% versus 11.4% six days after challenge). Interim conclusion Collectively, our studies to date are consistent with our proposal's hypothesis that a ME-depleted diet (ERD) increases the susceptibility of mice to challenge with C. difficile. The AIN-93G diet did not increase the susceptibility. We speculate that casein in AIN-93G provided contains MEs. Casein is not present in the ERD diet.

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Zempleni J. Novel bioactive compounds in milk: exosomes. Harold Hamm Diabetes Center at the University of Oklahoma, Oklahoma City, OK. March 21, 2022 [talk, delivered by Zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Wang S, Auchtung J, Zempleni J. Milk exosomes select mutations that decrease the toxicity of Clostridioides difficile. NPOD Annual Spring Research Retreat, April 19, 2022, Lincoln, NE
  • Type: Journal Articles Status: Other Year Published: 2022 Citation: Zhou, F, Dogan H, Madadjim R, Mumtaz PT, Cui J, Zempleni J. Divergence of gut bacteria through the selection of genetic variants by small extracellular vesicles in milk (in preparation)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2022 Citation: Wang S, Auchtung J, Zempleni J. Milk exosomes select mutations that decrease the toxicity of Clostridioides difficile. Nutrition 2022 Conference (virtual), American Society for Nutrition; 6/14  6/16, 2022 [virtual talk by Zoom]
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Ngu A, Wang S, Wang H, Khanam A, Zempleni J. Milk exosomes in nutrition and drug delivery. Am J Physiol Cell Physiol 322:C865-C874, 2022
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Munir J, Ngu A, Wang H, Ramirez DMO, Zempleni J. Review: Milk Small Extracellular Vesicles for Use in the Delivery of Therapeutics. Pharm Res (in press)
  • Type: Journal Articles Status: Other Year Published: 2022 Citation: Ngu A,* Munir J,* Zempleni J. Distribution and elimination of milk-borne small extracellular vesicles. (invited review, submitted)
  • Type: Journal Articles Status: Other Year Published: 2022 Citation: Wang S, Auchtung J, Zempleni J. Milk small extracellular vesicles select genetic variants that decrease the toxicity of Clostridioides difficile (in preparation)
  • Type: Journal Articles Status: Published Year Published: 2022 Citation: Sukreet S, Pereira Braga C, An, TT, Adamec J, Cui J, Zempleni J. Ultrasonication of milk decreases the content of exosomes and microRNAs in an exosome-defined rodent diet. J Nutr 152:961-970, 2022


Progress 03/15/21 to 03/14/22

Outputs
Target Audience:The target audience includes scientists (faculty, postdocs, students) in nutrition, biomedical science, policy makers, dairy industry, journalists and lay public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provides support for two faculty, Drs. J. Zempleni (PD) and J. Auchtung (co-PD), a postdoctoral associate (Dr. S. Wang) and a research technologist. Dr. Zempleni has acquired new knowledge in studies of microbiology, whereas Dr. Auchtung has acquired new knowledge in nutrition research, dairy and milk exosomes. The postdoctoral associate was new to both microbiology and milk exosome research and has acquired expertise in both areas. The technologist was new to milk exosome research and has acquired technical skills in that area. In future years we intend to have the postdoctoral associate present and Dr. Zempleni findings from this study at scientific conferences, which proved to be a challenge in Year 1 due to the COVID-19 pandemic. Drs. Zempleni and Wang have shared some of the findings though invited seminars and presentations at scientific conferences (see Products). How have the results been disseminated to communities of interest?Results have been disseminated through invited seminars and presentations at scientific conferences (see Products). What do you plan to do during the next reporting period to accomplish the goals?1. Challenge mice on ERS, ERD and AIN-93G diets with C. difficile that overexpress wild-type ptsG or ptsG_indel, and we have developed ptsG knockout C. difficile. 2. Sequence the genomes of E. faecalis selected in milk-exosome-defined media. 3. Perform cultures of gut content and assess milk exosome-dependent changes in the bacterial transcriptome and metabolome. 4.Test effects of defined diet feeding on susceptibility to E. faecalis infection in mice. 5. Repeat the studies in mice fed the AIN-93G diet (see above, Objective 3).

Impacts
What was accomplished under these goals? Objective 1. Objective 1. Assess the selection of polymorphisms in C. difficile and vancomycin-resistant E. faecalis in milk exosome-defined cultures. This objective tests the hypothesis that the presence of milk exosomes in culture will select for genetic polymorphisms that may enhance or diminish virulence-associated phenotypes that can be measured in vitro compared to bacteria prior to passaging (reference genome). This is our Year 2 report. In Year 1 we reported that milk exosomes selected a deletion in the phosphotransferase (PTS_EIIA_1) domain in the ptsG gene ("ptsG _indel"). The ptsG gene facilitates glucose transport in bacteria and is implicated in pathogenicity C. difficile. Exosome-selected C. difficile grew faster and produced less toxin than non-selected controls (see Objective 3). In this reporting period, we expanded these studies by developing strains of C. difficile that overexpress wild-type ptsG or ptsG_indel, and we have made progress towards developing ptsG knockout C. difficile. Using these strains, we started interrogating effects of ptsG overexpression on growth and toxin production. We observed that overexpression of ptsG_indel increased growth and reduced toxin production in C. difficile. This observation is consistent with our hypothesis that milk exosomes select for polymorphisms that decrease the pathogenicity of gut pathogens. In this reporting period, we also selected polymorphisms of vancomycin-resistant E. faecalis in milk exosome-defined cultures. While we have not yet sequenced the genomes of the isolates, we observed that E. faecalis selected in milk exosome-supplemented media led to increased doubling time in defined medium and biofilm production compared to control E. faecalis strains serially passaged in the absence of exosomes. Objective 2. Objective 2. Assess whether milk exosomes cause changes in the host microbiome that alter the colonization of mice with C. difficile and E. faecalis not selected in exosome cultures. This objective tests the hypothesis that feeding milk exosome and RNA-depleted (ERD) diets and milk exosome and RNA-sufficient (ERS) diets causes changes in microbial communities in the murine gut that alter the susceptibility to challenges with pathogens. In Year 1, we fed C57BL/6 mice milk exosome and RNA-depleted (ERD) diets and milk exosome and RNA-sufficient (ERS) diets for four weeks starting at age 3.5-4.5 weeks and challenged with an oral dose of 105 spores from C. difficile. The survival of mice fed the ERD diet decreased by approximately 50% compared to mice fed the ERS diet (P < 0.05). Consistent with this observation, median clinical sickness scores (B. Fehlhaber et al, Sci. Rep. 2019; 9: 5919; PMC6459866).in mice fed an ERD diet were 3-fold higher than mice fed the ERS (P < 0.01). In this reporting period, we assessed bacterial communities in mice fed ERD and ERS diets, with and without challenge by C. difficile by using 16S rRNA sequencing. We observed significant changes in a small number of taxa between treatment groups on day 3 followingC. difficilechallenge, with ERS diet selecting for increases inLachnospiraceae, Bacteroides(5OTUs) andAlistipes(2OTUs), and ERD diet selecting for increases inAkkermansia,Escherichia/Shigella,Enterococcaceae, andClostridiumsensustricto. Since strains elevated by ERD diet are often associated with increased disease severity (Escherichia/ShigellaandEnterococcaceae), we hypothesize that the primary effects of ERS diet are on the host response to infection as reduced disease severity may allow recovery of protective taxa and limit expansion of pathobionts. We also observed that myeloperoxidase activity, a marker of neutrophil infiltration was significantly higher in mice fed an ERD diet on day 7 of infection compared to mice fed an ERS diet, pointing to higher levels of inflammation in the absence of exosomes. While these results were potentially interesting, we also observed that disease severity differed between mice that were colonized with human microbes and conventional microbes and in mice colonized with human microbes over time, suggesting that interactions between exosomes and specific bacteria present in the microbiome are essential for disease progression. We conducted additional feeding studies and challenged the mice with C.difficile. seven days post C. difficile, the myeloperoxidase (MPO) activity, which was used to assess the neutrophil/granulocyte infiltration, was higher in cecum and colon from ERD-fed mice than that from ERS-fed mice; IL-17b was also higher in the colon from ERD-fed mice compared to ERS-fed mice. In this funding period we also submitted a manuscript detailing the ERD and ERS diets. The manuscript was returned to us for revision (in progress). Objective 3. Objective 3. Assess the pathogenicity of in vitro-selected polymorphisms in mice fed a regular AIN-93G diet. This objective tests the hypothesis that C. difficile and E. faecalis selected in milk exosome-free (E-Minus) cultures cause disease phenotypes that differ in severity compared to phenotypes caused by C. difficile and E. faecalis selected in milk exosome-supplemented (E-Plus) cultures. In Year 1, we selected C. difficile in a variety of milk exosome-defined media and compared growth rate and toxin production to C. difficile cultured in exosome-free media. The growth rate was assessed by measuring the bacteria's doubling time. C. difficile in milk exosome-containing media grew 15% to 20% faster than controls cultured in exosome-free media. However, the production of toxins, tcdA and tcdB, was 60% to 90% lower in the various milk exosome-containing cultures of C. difficile compared to exosome-free control cultures. Toxin production was assessed by using real-time PCR and by using cytotoxic effects in Vero cells (A. Valdiviesco-Garcia et al., 1993; 59: 1981-1983; PMC not available). In this reporting period, we added a dietary treatment group to our mouse feeding studies to include three dietary treatments: mice fed AIN-93G or ERS or ERD diets. Note that the ERD and ERS diets are based on the AIN-93G formulation, except that the ERD diet is depleted o milk exosomes and their RNA cargos. The mice were challenged with C. difficile and pathogenicity was assessed by monitoring the mortality, weight loss over the time, and measuring the C.difficile CFU and toxin activity present in the fecal samples. Results were inconclusive and we will repeat these studies in the next reporting period. That said, studies were successful in demonstrating that the minor content of lactose in experimental diets is not a confounder in studies of mice (which are lactose intolerant; see the manuscript by Sukreet et al. in Products).

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zempleni J. Biological Activities of Natural Nanoparticles (Exosomes) in Milk. Department of Ophthalmology, Penn State Hershey Medical Center, Hershey, PA. February 17, 2021 [talk, delivered by using Zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zempleni J. Novel bioactive compounds in milk: exosomes. Department of Animal Science, University of Nebraska-Lincoln, NE. April 6, 2021 [talk, delivered by using Zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zempleni J. Milk exosome-driven evolution of antibiotic-resistant gut pathogens. NIFA Program Directors Meeting, Kansas City, KS. May 4, 2021 [talk, delivered by using Zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Wang S, Auchtung J, Zempleni J. Milk exosomes select genetic variants that decrease the toxicity of Clostridioides difficile. NPOD 7th Annual Research Symposium, September 13th, 2021, Lincoln, NE [video poster, delivered by Zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zempleni J, Zhou F, Dogan H, Cui J. Divergence of gut bacteria through the selection of genetic variations by extracellular vesicles in milk. International Society for Extracellular Vesicles. Annual (virtual) conference, 5/18  5/21, 2021 [poster video presentation] J Extracell Vesicles:10 (Suppl. 1):e12083, 2021
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Wang S, Auchtung J, Zempleni J. Milk exosomes protect human microbiota associated-mice against Clostridioides difficile infection. Nutrition 2021 Conference (virtual), American Society for Nutrition; 6/7  6/11/2021
  • Type: Journal Articles Status: Accepted Year Published: 2021 Citation: Wang H, Wu D, Sukreet S, Delaney A, Belfort MB, Zempleni J. Quantitation of exosomes and their microRNA cargos in frozen human milk. JPGN Reports (in press)
  • Type: Journal Articles Status: Published Year Published: 2021 Citation: Ogunnaike M, Wang, H, Zempleni J. Bovine mammary alveolar MAC-T cells afford a tool for studies of bovine milk exosomes in drug delivery. Int J Pharm 610:121263, 2021
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Zhou, F, Dogan H, Shu J, Fernando SC, Cui J, Zempleni J. Evolution of gut bacteria through the selection of genetic variations by extracellular vesicles in milk (under revision)
  • Type: Journal Articles Status: Submitted Year Published: 2021 Citation: Sukreet S, Pereira Braga C, An, TT, Adamec J, Cui J, Zempleni J. Modification of the AIN-93G diet by substituting ultrasonicated milk for casein yields a rodent diet deplete of bioavailable milk exosomes and microRNAs (under revision)
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zempleni J, Zhou F, Dogan H, Cui J. Divergence of gut bacteria through the selection of genetic variations by milk exosomes. Keystone Virtual Symposia The Microbiome: From Mother to Child, January 17-21, 2021 [video poster, delivered by using Zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zempleni J. Invited presentation titled W-4002 progress report Zempleni lab: milk exosomes as part of the remote annual W-4002 Multistate group meeting; Ohio State University, Columbus, OH, January 27th, 2021 [talk]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2021 Citation: Zempleni J. Milk exosomes and their microRNA cargos: infants, gut and brain. Department of Nutritional Sciences, University of Michigan, MI. February 10, 2021 [talk, delivered by using Zoom]


Progress 03/15/20 to 03/14/21

Outputs
Target Audience:The target audience includes scientists (faculty, postdocs, students) in nutrition, biomedical science, policy makers, dairy industry, journalists and lay public. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?The project provides support for two faculty, Drs. J. Zempleni (PD) and J. Auchtung (co-PD), a postdoctoral associate (Dr. S. Wang) and a research technologist. Dr. Zempleni has acquired new knowledge in studies of microbiology, whereas Dr. Auchtung has acquired new knowledge in nutrition research, dairy and milk exosomes. The postdoctoral associate was new to both microbiology and milk exosome research and has acquired expertise in both areas. The technologist was new to milk exosome research and has acquired technical skills in that area. In future years we intend to have the postdoctoral associate present and Dr. Zempleni findings from this study at scientific conferences, which proved to be a challenge in Year 1 due to the COVID-19 pandemic. Dr. Zempleni has shared some of the findings at invited seminars at Chapman University and the University of Nebraska Medical Center (see Products). How have the results been disseminated to communities of interest?Results have been disseminated through NIFA blogs and Twitter (see Other Products) and invited seminars (see preceding paragraph). What do you plan to do during the next reporting period to accomplish the goals?1. Assess how variations in the ptsG gene alter the virulence of C. difficile. 2. Assess whether milk exosome-evolved C. difficile colonize the murine gut. 3. Assess the uptake of milk exosomes by gut bacteria. 4. Initiate studies in E. faecalis. 5. Perform cultures of gut content and assess milk exosome-dependent changes in the bacterial transcriptome and metabolome.

Impacts
What was accomplished under these goals? Objective 1.Assess the selection of polymorphisms inC.difficileand vancomycin-resistantE. faecalisin milk exosome-defined cultures. This objective tests the hypothesis that the presence of milk exosomes in culture will select for genetic polymorphisms that may enhance or diminish virulence-associated phenotypes that can be measuredin vitrocompared to bacteria prior to passaging (reference genome). To date we identified a moderate size deletion (~90 bp) in the phosphotransferase (PTS_EIIA_1) domain of the ptsG gene that was consistently present in exosome-evolved strains of Clostridioides difficile that were sequenced (n=6) compared to vehicle-evolved strains (n=3) and parental strain (n=1). We also identified a single base pair variation in the phosphotransferase (PTS_EIIA_1) domain of the ptsG gene in exosome-evolved strains of C. difficile compared to vehicle-evolved strains. The ptsG gene facilitates glucose transport in bacteria. Objective 2.Assess whether milk exosomes cause changes in the host microbiome that alter the colonization of mice withC. difficileandE. faecalisnot selected in exosome cultures. This objective tests the hypothesis that feeding milk exosome and RNA-depleted (ERD) diets and milk exosome and RNA-sufficient (ERS) diets causes changes in microbial communities in the murine gut that alter the susceptibility to challenges with pathogens. We have completed a first study in which we fed C57BL/6 mice milk exosome and RNA-depleted (ERD) diets and milk exosome and RNA-sufficient (ERS) diets for four weeks starting at age 3.5-4.5 weeks and challenged with an oral dose of 105 spores from C. difficile. The survival of mice fed the ERD diet decreased by approximately 50% compared to mice fed the ERS diet (P < 0.05). Consistent with this observation, median clinical sickness scores (B. Fehlhaber et al, Sci. Rep. 2019; 9: 5919; PMC6459866).in mice fed an ERD diet were 3-fold higher than mice fed the ERS (P < 0.01). Objective 3.Assess the pathogenicity ofin vitro-selected polymorphisms in mice fed a regular AIN-93G diet. This objective tests the hypothesis thatC. difficileandE. faecalisselected in milk exosome-free (E-Minus) cultures cause disease phenotypes that differ in severity compared to phenotypes caused byC. difficileandE. faecalisselected in milk exosome-supplemented (E-Plus) cultures. We selected C. difficile in a variety of milk exosome-defined media and compared growth rate and toxin production to C. difficile cultured in exosome-free media. The growth rate was assessed by measuring the bacteria's doubling time. C. difficile in milk exosome-containing media grew 15% to 20% faster than controls cultured in exosome-free media. However, the production of toxins, tcdA and tcdB, was 60% to 90% lower in the various milk exosome-containing cultures of C. difficile compared to exosome-free control cultures. Toxin production was assessed by using real-time PCR and by using cytotoxic effects in Vero cells (A. Valdiviesco-Garcia et al., 1993; 59: 1981-1983; PMC not available).

Publications

  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Zempleni J. Exosomes and microRNAs in maternal milk are important for growth and gut health during weaning in murine pups. Chapman University, CA. November 11, 2020 [talk, delivered by using Zoom]
  • Type: Conference Papers and Presentations Status: Published Year Published: 2020 Citation: Zempleni J. The role of milk exosomes and their RNA cargos in neonatal health. Life Span Diseases Mini Summit in the Child Health Research Institute, University of Nebraska Medical Center, November 13, 2020 [talk, delivered by using Zoom]