1
|
Narrowe AB, Lemons JMS, Mahalak KK, Firrman J, den Abbeele PV, Baudot A, Deyaert S, Li Y, Yu L(L, Liu L. Targeted remodeling of the human gut microbiome using Juemingzi ( Senna seed extracts). Front Cell Infect Microbiol 2024; 14:1296619. [PMID: 38638830 PMCID: PMC11024242 DOI: 10.3389/fcimb.2024.1296619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 03/19/2024] [Indexed: 04/20/2024] Open
Abstract
The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi (Senna sp.) extract on the human gut microbiome using SIFR® (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and post-incubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi (Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome.
Collapse
Affiliation(s)
- Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | | | | | | | - Yanfang Li
- Department of Nutrition and Food Science, The University of Maryland, College, Park, MD, United States
| | - Liangli (Lucy) Yu
- Department of Nutrition and Food Science, The University of Maryland, College, Park, MD, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| |
Collapse
|
2
|
Narrowe AB, Liu L, Lemons JMS, Firrman JA, Mahalak KK, Deyaert S, Baudot A, Van den Abbeele P. Metagenomes and metagenome-assembled genomes from ex vivo fecal incubations of six unique donors. Microbiol Resour Announc 2024; 13:e0086223. [PMID: 38236043 PMCID: PMC10868202 DOI: 10.1128/mra.00862-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024] Open
Abstract
We present a donor-specific collection of 78 metagenomes (13/donor) and 143 metagenome-assembled genomes (MAGs), representing the gut microbiomes of six healthy adult human donors. In addition to adding to the catalog of publicly available human gut MAGs, this resource permits a genome-resolved look into microbial co-occurrence across six individuals.
Collapse
Affiliation(s)
- Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Jenni A. Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | - Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, Pennsylvania, USA
| | | | | | | |
Collapse
|
3
|
Lemons JMS. Too Much of a Good Thing: Imposing an Upper Limit to a High Fiber Diet. Gastroenterology 2024; 166:250-251. [PMID: 38008229 DOI: 10.1053/j.gastro.2023.11.290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 11/28/2023]
Affiliation(s)
- Johanna M S Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, Pennsylvania.
| |
Collapse
|
4
|
Lemons JMS, Narrowe AB, Liu L, Firrman J, Mahalak KK, Van den Abbeele P, Baudot A, Deyaert S, Li Y, Yu L(L. Impact of Baizhu, Daqingye, and Hehuanhua extracts on the human gut microbiome. Front Cell Infect Microbiol 2023; 13:1298392. [PMID: 38145049 PMCID: PMC10740150 DOI: 10.3389/fcimb.2023.1298392] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 11/23/2023] [Indexed: 12/26/2023] Open
Abstract
Introduction In traditional Chinese medicine, the rhizome of Atractylodes macrocephala (Baizhu), the leaves of Isatis indigotica (Daqingye), and the flowers of Albizia julibrissin (Hehuanhua) have been used to treat gastrointestinal illnesses, epidemics, and mental health issues. Modern researchers are now exploring the underlying mechanisms responsible for their efficacy. Previous studies often focused on the impact of purified chemicals or mixed extracts from these plants on cells in tissue culture or in rodent models. Methods As modulation of the human gut microbiome has been linked to host health status both within the gastrointestinal tract and in distant tissues, the effects of lipid-free ethanol extracts of Baizhu, Daqingye, and Hehuanhua on the human adult gut microbiome were assessed using Systemic Intestinal Fermentation Research (SIFR®) technology (n=6). Results and discussion Baizhu and Daqingye extracts similarly impacted microbial community structure and function, with the extent of effects being more pronounced for Baizhu. These effects included decreases in the Bacteroidetes phylum and increases in health-related Bifidobacterium spp. and short chain fatty acids which may contribute to Baizhu's efficacy against gastrointestinal ailments. The changes upon Hehuanhua treatment were larger and included increases in multiple bacterial species, including Agathobaculum butyriciproducens, Adlercreutzia equolifaciens, and Gordonibacter pamelaeae, known to produce secondary metabolites beneficial to mental health. In addition, many of the changes induced by Hehuanhua correlated with a rise in Enterobacteriaceae spp., which may make the tested dose of this herb contraindicated for some individuals. Overall, there is some evidence to suggest that the palliative effect of these herbs may be mediated, in part, by their impact on the gut microbiome, but more research is needed to elucidate the exact mechanisms.
Collapse
Affiliation(s)
- Johanna M. S. Lemons
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - Adrienne B. Narrowe
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - LinShu Liu
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - Jenni Firrman
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | - Karley K. Mahalak
- United States Department of Agriculture, Agricultural Research Service, Eastern Regional Research Center, Dairy and Functional Foods Research Unit, Wyndmoor, PA, United States
| | | | | | | | - Yanfang Li
- Department of Nutrition and Food Science, 0112 Skinner Building University of Maryland, College Park, MD, United States
| | - Liangli (Lucy) Yu
- Department of Nutrition and Food Science, 0112 Skinner Building University of Maryland, College Park, MD, United States
| |
Collapse
|
5
|
Liu L, Mahalak KK, Bobokalonov JT, Narrowe AB, Firrman J, Lemons JMS, Bittinger K, Hu W, Jones SM, Moustafa AM. Impact of Ivermectin on the Gut Microbial Ecosystem. Int J Mol Sci 2023; 24:16125. [PMID: 38003317 PMCID: PMC10671733 DOI: 10.3390/ijms242216125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/02/2023] [Accepted: 11/04/2023] [Indexed: 11/26/2023] Open
Abstract
Ivermectin is a an anti-helminthic that is critical globally for both human and veterinary care. To the best of our knowledge, information available regarding the influence of ivermectin (IVM) on the gut microbiota has only been collected from diseased donors, who were treated with IVM alone or in combination with other medicines. Results thus obtained were influenced by multiple elements beyond IVM, such as disease, and other medical treatments. The research presented here investigated the impact of IVM on the gut microbial structure established in a Triple-SHIME® (simulator of the human intestinal microbial ecosystem), using fecal material from three healthy adults. The microbial communities were grown using three different culture media: standard SHIME media and SHIME media with either soluble or insoluble fiber added (control, SF, ISF). IVM introduced minor and temporary changes to the gut microbial community in terms of composition and metabolite production, as revealed by 16S rRNA amplicon sequencing analysis, flow cytometry, and GC-MS. Thus, it was concluded that IVM is not expected to induce dysbiosis or yield adverse effects if administered to healthy adults. In addition, the donor's starting community influences the relationship between IVM and the gut microbiome, and the soluble fiber component in feed could protect the gut microbiota from IVM; an increase in short-chain fatty acid production was predicted by PICRUSt2 and detected with IVM treatment.
Collapse
Affiliation(s)
- LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Jamshed T. Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steven M. Jones
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ahmed M. Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
6
|
Lemons JMS, Conrad M, Tanes C, Chen J, Friedman ES, Roggiani M, Curry D, Chau L, Hecht AL, Harling L, Vales J, Kachelries KE, Baldassano RN, Goulian M, Bittinger K, Master SR, Liu L, Wu GD. Enterobacteriaceae Growth Promotion by Intestinal Acylcarnitines, a Biomarker of Dysbiosis in Inflammatory Bowel Disease. Cell Mol Gastroenterol Hepatol 2023; 17:131-148. [PMID: 37739064 PMCID: PMC10694575 DOI: 10.1016/j.jcmgh.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023]
Abstract
BACKGROUND & AIMS Altered plasma acylcarnitine levels are well-known biomarkers for a variety of mitochondrial fatty acid oxidation disorders and can be used as an alternative energy source for the intestinal epithelium when short-chain fatty acids are low. These membrane-permeable fatty acid intermediates are excreted into the gut lumen via bile and are increased in the feces of patients with inflammatory bowel disease (IBD). METHODS Herein, based on studies in human subjects, animal models, and bacterial cultures, we show a strong positive correlation between fecal carnitine and acylcarnitines and the abundance of Enterobacteriaceae in IBD where they can be consumed by bacteria both in vitro and in vivo. RESULTS Carnitine metabolism promotes the growth of Escherichia coli via anaerobic respiration dependent on the cai operon, and acetylcarnitine dietary supplementation increases fecal carnitine levels with enhanced intestinal colonization of the enteric pathogen Citrobacter rodentium. CONCLUSIONS In total, these results indicate that the increased luminal concentrations of carnitine and acylcarnitines in patients with IBD may promote the expansion of pathobionts belonging to the Enterobacteriaceae family, thereby contributing to disease pathogenesis.
Collapse
Affiliation(s)
- Johanna M S Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania
| | - Maire Conrad
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jie Chen
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elliot S Friedman
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Manuela Roggiani
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Dylan Curry
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lillian Chau
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Aaron L Hecht
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Lisa Harling
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer Vales
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Kelly E Kachelries
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Robert N Baldassano
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Mark Goulian
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Stephen R Master
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, Pennsylvania.
| | - Gary D Wu
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.
| |
Collapse
|
7
|
Liu L, Narrowe AB, Firrman JA, Mahalak KK, Bobokalonov JT, Lemons JMS, Bittinger K, Daniel S, Tanes C, Mattei L, Friedman ES, Soares JW, Kobori M, Zeng WB, Tomasula PM. Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME). Foods 2023; 12:2105. [PMID: 37297350 PMCID: PMC10252382 DOI: 10.3390/foods12112105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/13/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
In the present research, we investigated changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). The probiotics were added to the ascending colon region of mature microbial communities established in a human intestinal microbial ecosystem simulator. Shotgun metagenomic sequencing and metabolome analysis suggested that the changes in microbial community composition corresponded with changes to metabolic output, and we can infer linkages between some metabolites and microorganisms. The in vitro method permits a spatially-resolved view of metabolic transformations under human physiological conditions. By this method, we found that tryptophan and tyrosine were mainly produced in the ascending colon region, while their derivatives were detected in the transverse and descending regions, revealing sequential amino acid metabolic pathways along with the colonic tract. The addition of LGG appeared to promote the production of indole propionic acid, which is positively associated with human health. Furthermore, the microbial community responsible for the production of indole propionic acid may be broader than is currently known.
Collapse
Affiliation(s)
- LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Jenni A. Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Jamshed T. Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
- V.I. Nikitin Chemistry Institute of Tajikistan Academy of Sciences, Dushanbe 734063, Tajikistan
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elliot S. Friedman
- Division of Gastroenterology & Hepatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jason W. Soares
- Bioprocessing and Bioengineering Group, US Army Combat Capabilities Development Command Soldier Center (CCDC-SC), Natick, MA 01760, USA
| | - Masuko Kobori
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba 305-8642, Ibaraki, Japan
| | - Wei-Bin Zeng
- Department of Mathematics, University of Louisville, Louisville, KY 40292, USA
| | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA 19038, USA
| |
Collapse
|
8
|
Mahalak KK, Firrman J, Bobokalonov J, Narrowe AB, Bittinger K, Daniel S, Tanes C, Mattei LM, Zeng WB, Soares JW, Kobori M, Lemons JMS, Tomasula PM, Liu L. Persistence of the Probiotic Lacticaseibacillus rhamnosus Strain GG (LGG) in an In Vitro Model of the Gut Microbiome. Int J Mol Sci 2022; 23:12973. [PMID: 36361763 PMCID: PMC9657340 DOI: 10.3390/ijms232112973] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/26/2023] Open
Abstract
The consumption of probiotics is widely encouraged due to reports of their positive effects on human health. In particular, Lacticaseibacillus rhamnosus strain GG (LGG) is an approved probiotic that has been reported to improve health outcomes, especially for gastrointestinal disorders. However, how LGG cooperates with the gut microbiome has not been fully explored. To understand the interaction between LGG and its ability to survive and grow within the gut microbiome, this study introduced LGG into established microbial communities using an in vitro model of the colon. LGG was inoculated into the simulated ascending colon and its persistence in, and transit through the subsequent transverse and descending colon regions was monitored over two weeks. The impact of LGG on the existing bacterial communities was investigated using 16S rRNA sequencing and short-chain fatty acid analysis. LGG was able to engraft and proliferate in the ascending region for at least 10 days but was diminished in the transverse and descending colon regions with little effect on short-chain fatty acid abundance. These data suggest that the health benefits of the probiotic LGG rely on its ability to transiently engraft and modulate the host microbial community.
Collapse
Affiliation(s)
- Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Jamshed Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Scott Daniel
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Ceylan Tanes
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lisa M. Mattei
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Wei-Bin Zeng
- Department of Mathematics, University of Louisville, Louisville, KY 40292, USA
| | - Jason W. Soares
- Bioprocessing and Bioengineering Group, US Army Combat Capabilities Development Command Soldier Center (CCDC-SC), Natick, MA 01760, USA
| | - Masuko Kobori
- Institute of Food Research, National Agriculture and Food Research Organization, Tsukuba 305-8642, Ibaraki, Japan
| | - Johanna M. S. Lemons
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - Peggy M. Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA 19038, USA
| |
Collapse
|
9
|
Suh EJ, Remillard MY, Legesse-Miller A, Johnson EL, Lemons JMS, Chapman TR, Forman JJ, Kojima M, Silberman ES, Coller HA. A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts. Genome Biol 2012; 13:R121. [PMID: 23259597 PMCID: PMC3924601 DOI: 10.1186/gb-2012-13-12-r121] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/22/2012] [Indexed: 01/01/2023] Open
Abstract
Background Although quiescence (reversible cell cycle arrest) is a key part in the life history and fate of many mammalian cell types, the mechanisms of gene regulation in quiescent cells are poorly understood. We sought to clarify the role of microRNAs as regulators of the cellular functions of quiescent human fibroblasts. Results Using microarrays, we discovered that the expression of the majority of profiled microRNAs differed between proliferating and quiescent fibroblasts. Fibroblasts induced into quiescence by contact inhibition or serum starvation had similar microRNA profiles, indicating common changes induced by distinct quiescence signals. By analyzing the gene expression patterns of microRNA target genes with quiescence, we discovered a strong regulatory function for miR-29, which is downregulated with quiescence. Using microarrays and immunoblotting, we confirmed that miR-29 targets genes encoding collagen and other extracellular matrix proteins and that those target genes are induced in quiescence. In addition, overexpression of miR-29 resulted in more rapid cell cycle re-entry from quiescence. We also found that let-7 and miR-125 were upregulated in quiescent cells. Overexpression of either one alone resulted in slower cell cycle re-entry from quiescence, while the combination of both together slowed cell cycle re-entry even further. Conclusions microRNAs regulate key aspects of fibroblast quiescence including the proliferative state of the cells as well as their gene expression profiles, in particular, the induction of extracellular matrix proteins in quiescent fibroblasts.
Collapse
|
10
|
Legesse-Miller A, Raitman I, Haley EM, Liao A, Sun LL, Wang DJ, Krishnan N, Lemons JMS, Suh EJ, Johnson EL, Lund BA, Coller HA. Quiescent fibroblasts are protected from proteasome inhibition-mediated toxicity. Mol Biol Cell 2012; 23:3566-81. [PMID: 22875985 PMCID: PMC3442405 DOI: 10.1091/mbc.e12-03-0192] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Proteasome inhibition is used as a treatment strategy for multiple types of cancers. Although proteasome inhibition can induce apoptotic cell death in actively proliferating cells, it is less effective in quiescent cells. In this study, we used primary human fibroblasts as a model system to explore the link between the proliferative state of a cell and proteasome inhibition-mediated cell death. We found that proliferating and quiescent fibroblasts have strikingly different responses to MG132, a proteasome inhibitor; proliferating cells rapidly apoptosed, whereas quiescent cells maintained viability. Moreover, MG132 treatment of proliferating fibroblasts led to increased superoxide anion levels, juxtanuclear accumulation of ubiquitin- and p62/SQSTM1-positive protein aggregates, and apoptotic cell death, whereas MG132-treated quiescent cells displayed fewer juxtanuclear protein aggregates, less apoptosis, and higher levels of mitochondrial superoxide dismutase. In both cell states, reducing reactive oxygen species with N-acetylcysteine lessened protein aggregation and decreased apoptosis, suggesting that protein aggregation promotes apoptosis. In contrast, increasing cellular superoxide levels with 2-methoxyestradiol treatment or inhibition of autophagy/lysosomal pathways with bafilomycin A1 sensitized serum-starved quiescent cells to MG132-induced apoptosis. Thus, antioxidant defenses and the autophagy/lysosomal pathway protect serum-starved quiescent fibroblasts from proteasome inhibition-induced cytotoxicity.
Collapse
|
11
|
Abstract
Quiescence is a state of reversible cell cycle arrest that can grant protection against many environmental insults. In some systems, cellular quiescence is associated with a low metabolic state characterized by a decrease in glucose uptake and glycolysis, reduced translation rates and activation of autophagy as a means to provide nutrients for survival. For cells in multiple different quiescence model systems, including Saccharomyces cerevisiae, mammalian lymphocytes and hematopoietic stem cells, the PI3Kinase/TOR signaling pathway helps to integrate information about nutrient availability with cell growth rates. Quiescence signals often inactivate the TOR kinase, resulting in reduced cell growth and biosynthesis. However, quiescence is not always associated with reduced metabolism; it is also possible to achieve a state of cellular quiescence in which glucose uptake, glycolysis and flux through central carbon metabolism are not reduced. In this review, we compare and contrast the metabolic changes that occur with quiescence in different model systems.
Collapse
Affiliation(s)
- James R Valcourt
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | | | | | | | | |
Collapse
|
12
|
Guo JY, Chen HY, Mathew R, Fan J, Strohecker AM, Karsli-Uzunbas G, Kamphorst JJ, Chen G, Lemons JMS, Karantza V, Coller HA, Dipaola RS, Gelinas C, Rabinowitz JD, White E. Activated Ras requires autophagy to maintain oxidative metabolism and tumorigenesis. Genes Dev 2011; 25:460-70. [PMID: 21317241 DOI: 10.1101/gad.2016311] [Citation(s) in RCA: 986] [Impact Index Per Article: 75.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Autophagy is a catabolic pathway used by cells to support metabolism in response to starvation and to clear damaged proteins and organelles in response to stress. We report here that expression of a H-ras(V12) or K-ras(V12) oncogene up-regulates basal autophagy, which is required for tumor cell survival in starvation and in tumorigenesis. In Ras-expressing cells, defective autophagosome formation or cargo delivery causes accumulation of abnormal mitochondria and reduced oxygen consumption. Autophagy defects also lead to tricarboxylic acid (TCA) cycle metabolite and energy depletion in starvation. As mitochondria sustain viability of Ras-expressing cells in starvation, autophagy is required to maintain the pool of functional mitochondria necessary to support growth of Ras-driven tumors. Human cancer cell lines bearing activating mutations in Ras commonly have high levels of basal autophagy, and, in a subset of these, down-regulating the expression of essential autophagy proteins impaired cell growth. As cancers with Ras mutations have a poor prognosis, this "autophagy addiction" suggests that targeting autophagy and mitochondrial metabolism are valuable new approaches to treat these aggressive cancers.
Collapse
|
13
|
Wellen KE, Lu C, Mancuso A, Lemons JMS, Ryczko M, Dennis JW, Rabinowitz JD, Coller HA, Thompson CB. The hexosamine biosynthetic pathway couples growth factor-induced glutamine uptake to glucose metabolism. Genes Dev 2010; 24:2784-99. [PMID: 21106670 DOI: 10.1101/gad.1985910] [Citation(s) in RCA: 282] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Glucose and glutamine serve as the two primary carbon sources in proliferating cells, and uptake of both nutrients is directed by growth factor signaling. Although either glucose or glutamine can potentially support mitochondrial tricarboxylic acid (TCA) cycle integrity and ATP production, we found that glucose deprivation led to a marked reduction in glutamine uptake and progressive cellular atrophy in multiple mammalian cell types. Despite the continuous presence of growth factor and an abundant supply of extracellular glutamine, interleukin-3 (IL-3)-dependent cells were unable to maintain TCA cycle metabolite pools or receptor-dependent signal transduction when deprived of glucose. This was due at least in part to down-regulation of IL-3 receptor α (IL-3Rα) surface expression in the absence of glucose. Treatment of glucose-starved cells with N-acetylglucosamine (GlcNAc) to maintain hexosamine biosynthesis restored mitochondrial metabolism and cell growth by promoting IL-3-dependent glutamine uptake and metabolism. Thus, glucose metabolism through the hexosamine biosynthetic pathway is required to sustain sufficient growth factor signaling and glutamine uptake to support cell growth and survival.
Collapse
Affiliation(s)
- Kathryn E Wellen
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | | | | | | | | | | | | | | | | |
Collapse
|