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Singh G, Brim H, Haileselassie Y, Varma S, Habtezion A, Rashid M, Sinha SR, Ashktorab H. Microbiomic and Metabolomic Analyses Unveil the Protective Effect of Saffron in a Mouse Colitis Model. Curr Issues Mol Biol 2023; 45:5558-5574. [PMID: 37504267 PMCID: PMC10378474 DOI: 10.3390/cimb45070351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 07/29/2023] Open
Abstract
Despite the existence of effective drugs used to treat inflammatory bowel disease (IBD), many patients fail to respond or lose response over time. Further, many drugs can carry serious adverse effects, including increased risk of infections and malignancies. Saffron (Crocus sativus) has been reported to have anti-inflammatory properties. Its protective role in IBD and how the microbiome and metabolome play a role has not been explored extensively. We aimed to establish whether saffron treatment modulates the host microbiome and metabolic profile in experimental colitis. Colitis was induced in C57BL/6 mice with 3% DSS and treated with either saffron in a dose of 20 mg/kg body weight or vehicle through daily gavage. On day 10, stool pellets from mice were collected and analyzed to assess saffron's effect on fecal microbiota and metabolites through 16S rRNA sequencing and untargeted primary metabolite analysis. Saffron treatment maintained gut microbiota homeostasis by counter-selecting pro-inflammatory bacteria and maintained Firmicutes/Bacteroides ratio, which was otherwise disturbed by DSS treatment. Several metabolites (uric acid, cholesterol, 2 hydroxyglutaric acid, allantoic acid, 2 hydroxyhexanoic acid) were altered significantly with saffron treatment in DSS-treated mice, and this might play a role in mediating saffron's colitis-mitigating effects. These data demonstrate saffron's therapeutic potential, and its protective role is modulated by gut microbiota, potentially acting through changes in metabolites.
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Affiliation(s)
- Gulshan Singh
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Hassan Brim
- Department of Pathology, Howard University College of Medicine, Washington, DC 20059, USA
| | - Yeneneh Haileselassie
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Sudhir Varma
- Hithru Analytics LLC, Silver Spring, MD 20877, USA
| | - Aida Habtezion
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Mudasir Rashid
- Department of Pathology and Cancer Center, College of Medicine, Howard University College of Medicine, Washington, DC 20059, USA
| | - Sidhartha R. Sinha
- Division of Gastroenterology and Hepatology, School of Medicine, Stanford University, Palo Alto, CA 94305, USA
| | - Hassan Ashktorab
- Department of Pathology and Cancer Center, College of Medicine, Howard University College of Medicine, Washington, DC 20059, USA
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Liu J, Ma X, Zhuo Y, Xu S, Hua L, Li J, Feng B, Fang Z, Jiang X, Che L, Zhu Z, Lin Y, Wu D. The Effects of Bacillus subtilis QST713 and β-mannanase on growth performance, intestinal barrier function, and the gut microbiota in weaned piglets. J Anim Sci 2023; 101:skad257. [PMID: 37583344 PMCID: PMC10449409 DOI: 10.1093/jas/skad257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/08/2023] [Indexed: 08/17/2023] Open
Abstract
We investigated the effects of different Bacillus subtilis QST713 doses and a B. subtilis QST713 and β-mannanase mix on growth performance, intestinal barrier function, and gut microbiota in weaned piglets. In total, 320 healthy piglets were randomly assigned to four groups: 1) control group (basal diet), 2) BS100 group (basal diet plus 100 mg/kg B. subtilis QST713), 3) BS200 group (basal diet plus 200 mg/kg B. subtilis QST713), and 4) a BS100XT group (basal diet plus 100 mg/kg B. subtilis QST713 and 150 mg/kg β-mannanase). The study duration was 42 d. We showed that feed intake in weaned piglets on days 1 to 21 was increased in group BS100 (P < 0.05), and that the feed conversion ratio in group BS100XT animals decreased throughout the study (P < 0.05). In terms of microbial counts, the BS100XT group showed reduced Escherichia coli and Clostridium perfringens numbers on day 21 (P < 0.05). Moreover, no significant α-diversity differences were observed across all groups during the study (P > 0.05). However, principal coordinates analysis indicated clear separations in bacterial community structures across groups (analysis of similarities: P < 0.05) on days 21 and 42. Additionally, E-cadherin, occludin, and zonula occludens-1 (ZO-1) expression in piglet feces increased (P < 0.05) by adding B. subtilis QST713 and β-mannanase to diets. Notably, this addition decreased short-chain fatty acid concentrations. In conclusion, B. subtilis QST713 addition or combined B. subtilis QST713 plus β-mannanase effectively improved growth performance, intestinal barrier function, and microbial balance in weaned piglets.
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Affiliation(s)
- Junchen Liu
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiangyuan Ma
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yong Zhuo
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Shengyu Xu
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Lun Hua
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jian Li
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Bin Feng
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Zhengfeng Fang
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xuemei Jiang
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Lianqiang Che
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Zeyuan Zhu
- Elanco Animal Health, Mutiara Damansara, Selangor, Malaysia
| | - Yan Lin
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - De Wu
- Institute of Animal Nutrition, Key Laboratory for Animal Disease-Resistance Nutrition of China, Ministry of Education, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
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Karagas MR, McRitchie S, Hoen AG, Takigawa C, Jackson B, Baker ER, Madan J, Sumner SJ, Pathmasiri W. Alterations in Microbial-Associated Fecal Metabolites in Relation to Arsenic Exposure Among Infants. EXPOSURE AND HEALTH 2022; 14:941-949. [PMID: 36776720 PMCID: PMC9918239 DOI: 10.1007/s12403-022-00468-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/09/2021] [Accepted: 01/22/2022] [Indexed: 05/13/2023]
Abstract
In utero and early life exposure to inorganic arsenic (iAs) alters immune response in experimental animals and is associated with an increased risk of infant infections. iAs exposure is related to differences in the gut microbiota diversity, community structure, and the relative abundance of individual microbial taxa both in laboratory and human studies. Metabolomics permits a direct measure of molecular products of microbial and host metabolic processes. We conducted NMR metabolomics analysis on infant stool samples and quantified the relative concentrations of 34 known microbial-related metabolites. We examined these metabolites in relation to both in utero and infant log2 urinary total arsenic concentrations (utAs, the sum of iAs and iAs metabolites) collected at approximately 6 weeks of age using linear regression models, adjusted for infant sex, age at sample collection, type of delivery (vaginal vs. cesarean section), feeding mode (breast milk vs. any formula), and specific gravity. Increased fecal butyrate (b = 214.24), propionate (b = 518.33), cholate (b = 8.79), tryptophan (b= 14.23), asparagine (b = 28.80), isoleucine (b = 65.58), leucine (b = 95.91), malonate (b = 50.43), and uracil (b = 36.13), concentrations were associated with a doubling of infant utAs concentrations (p< 0.05). These associations were largely among infants who were formula fed. No clear associations were observed with maternal utAs and infant fecal metabolites. Metabolomic analyses of infant stool samples lend further evidence that the infant gut microbiota is sensitive to As exposure, and these effects may have functional consequences.
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Affiliation(s)
- Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Susan McRitchie
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Anne G. Hoen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Cindy Takigawa
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Brian Jackson
- Department of Earth Sciences, Dartmouth College, Hanover, NH, USA
| | - Emily R. Baker
- Department of Obstetrics and Gynecology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Juliette Madan
- Department of Epidemiology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
- Department of Pediatrics & Psychiatry, Children’s Hospital at Dartmouth, Dartmouth Hitchcock Medical Center, Lebanon, NH, USA
| | - Susan J. Sumner
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wimal Pathmasiri
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Zhou J, Hoen AG, Mcritchie S, Pathmasiri W, Viles WD, Nguyen QP, Madan JC, Dade E, Karagas MR, Gui J. Information enhanced model selection for Gaussian graphical model with application to metabolomic data. Biostatistics 2022; 23:926-948. [PMID: 33720330 PMCID: PMC9608647 DOI: 10.1093/biostatistics/kxab006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 11/12/2022] Open
Abstract
In light of the low signal-to-noise nature of many large biological data sets, we propose a novel method to learn the structure of association networks using Gaussian graphical models combined with prior knowledge. Our strategy includes two parts. In the first part, we propose a model selection criterion called structural Bayesian information criterion, in which the prior structure is modeled and incorporated into Bayesian information criterion. It is shown that the popular extended Bayesian information criterion is a special case of structural Bayesian information criterion. In the second part, we propose a two-step algorithm to construct the candidate model pool. The algorithm is data-driven and the prior structure is embedded into the candidate model automatically. Theoretical investigation shows that under some mild conditions structural Bayesian information criterion is a consistent model selection criterion for high-dimensional Gaussian graphical model. Simulation studies validate the superiority of the proposed algorithm over the existing ones and show the robustness to the model misspecification. Application to relative concentration data from infant feces collected from subjects enrolled in a large molecular epidemiological cohort study validates that metabolic pathway involvement is a statistically significant factor for the conditional dependence between metabolites. Furthermore, new relationships among metabolites are discovered which can not be identified by the conventional methods of pathway analysis. Some of them have been widely recognized in biological literature.
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Affiliation(s)
- Jie Zhou
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, 3 Rope Ferry Road, Hanover, NH 03755, USA
| | - Anne G Hoen
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA and Depatment of Epidemiology, Geisel School of Medicine, Dartmouth College, 3 Rope Ferry Road, Hanover, NH 03755, USA
| | - Susan Mcritchie
- Nutrition Research Institute, Department of Nutrition, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081, USA
| | - Wimal Pathmasiri
- Nutrition Research Institute, Department of Nutrition, School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, 500 Laureate Way, Kannapolis, NC 28081, USA
| | - Weston D Viles
- Department of Mathematics and Statistics, University of Southern Maine, 96 Falmouth St, Portland, ME 04103, USA
| | - Quang P Nguyen
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA and Depatment of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Juliette C Madan
- Depatment of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Erika Dade
- Depatment of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Margaret R Karagas
- Depatment of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | - Jiang Gui
- Department of Biomedical Data Science, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
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The Tissue-Associated Microbiota in Colorectal Cancer: A Systematic Review. Cancers (Basel) 2022; 14:cancers14143385. [PMID: 35884445 PMCID: PMC9317273 DOI: 10.3390/cancers14143385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022] Open
Abstract
Simple Summary Growing evidence shows a close relationship between the microbiome and colorectal cancer, but most studies analyze fecal samples. However, solid information on the microbial community that is present locally in the intestinal tumor tissues is lacking. Therefore, the aim of this systematic review was to compile evidence on the relationship between tissue-associated microbiota and colorectal cancer. Among 5080 screened publications, 39 were eligible and included in the analysis. Despite the heterogeneity in methodologies and reporting between studies, 12 groups of bacteria with strong positive and 18 groups of bacteria with strong negative associations with colorectal cancer were identified. Such knowledge may ultimately be used in novel strategies that aim to prevent, detect, and treat colorectal cancer in the upcoming years. Abstract The intestinal microbiome is associated with colorectal cancer. Although the mucosal microbiota better represents an individual’s local microbiome, studies on the colorectal cancer microbiota mainly reflect knowledge obtained from fecal samples. This systematic review aimed to summarize the current evidence on the relationship between the mucosal-associated bacterial microbiota and colorectal cancer. Searches were conducted in PubMed and Web of Science databases for publications comparing the mucosal microbiome of colorectal cancer patients with that of healthy controls, or with that of non-cancerous mucosal tissues. The primary outcomes were differences in microbial diversity and taxonomy. The Newcastle-Ottawa Scale was used to assess the quality of the included studies. Of the 5080 studies identified, 39 were eligible and included in the systematic review. No consistent results were identified for the α- and β-diversity, due to high heterogeneity in reporting and to differences in metrics and statistical approaches, limiting study comparability. Qualitative synthesis of microbial taxonomy identified 12 taxa with strong positive and 18 taxa with strong negative associations with colorectal cancer. Fusobacterium, Campylobacter, Parvimonas, Peptostreptococcus, Streptococcus, and Granulicatella were defined as enriched in colorectal cancer. Despite the methodological limitations of the studies, consistent evidence on bacterial taxa associated with colorectal cancer was identified. Prospective studies in large and well-characterized patient populations will be crucial to validate these findings.
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Ahmad S, Ashktorab H, Brim H, Housseau F. Inflammation, microbiome and colorectal cancer disparity in African-Americans: Are there bugs in the genetics? World J Gastroenterol 2022; 28:2782-2801. [PMID: 35978869 PMCID: PMC9280725 DOI: 10.3748/wjg.v28.i25.2782] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 01/27/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023] Open
Abstract
Dysregulated interactions between host inflammation and gut microbiota over the course of life increase the risk of colorectal cancer (CRC). While environmental factors and socio-economic realities of race remain predominant contributors to CRC disparities in African-Americans (AAs), this review focuses on the biological mediators of CRC disparity, namely the under-appreciated influence of inherited ancestral genetic regulation on mucosal innate immunity and its interaction with the microbiome. There remains a poor understanding of mechanisms linking immune-related genetic polymorphisms and microbiome diversity that could influence chronic inflammation and exacerbate CRC disparities in AAs. A better understanding of the relationship between host genetics, bacteria, and CRC pathogenesis will improve the prediction of cancer risk across race/ethnicity groups overall.
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Affiliation(s)
- Sami Ahmad
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, DC 20060, United States
| | - Hassan Brim
- Department of Pathology, Howard University, Washington, DC 20060, United States
| | - Franck Housseau
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21231, United States
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Association of Cesarean Delivery and Formula Supplementation with the Stool Metabolome of 6-Week-Old Infants. Metabolites 2021; 11:metabo11100702. [PMID: 34677417 PMCID: PMC8540440 DOI: 10.3390/metabo11100702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 10/08/2021] [Accepted: 10/09/2021] [Indexed: 12/15/2022] Open
Abstract
Cesarean delivery and formula feeding have both been implicated as important factors associated with perturbations to the infant gut microbiome. To investigate the functional metabolic response of the infant gut microbial milieu to these factors, we profiled the stool metabolomes of 121 infants from a US pregnancy cohort study at approximately 6 weeks of life and evaluated associations with delivery mode and feeding method. Multivariate analysis of six-week stool metabolomic profiles indicated discrimination by both delivery mode and diet. For diet, exclusively breast-fed infants exhibited metabolomic profiles that were distinct from both exclusively formula-fed and combination-fed infants, which were relatively more similar to each other in metabolomic profile. We also identified individual metabolites that were important for differentiating delivery mode groups and feeding groups and metabolic pathways related to delivery mode and feeding type. We conclude based on previous work and this current study that the microbial communities colonizing the gastrointestinal tracts of infants are not only taxonomically, but also functionally distinct when compared according to delivery mode and feeding groups. Further, different sets of metabolites and metabolic pathways define delivery mode and diet metabotypes.
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Brim H, Taylor J, Abbas M, Vilmenay K, Daremipouran M, Varma S, Lee E, Pace B, Song-Naba WL, Gupta K, Nekhai S, O’Neil P, Ashktorab H. The gut microbiome in sickle cell disease: Characterization and potential implications. PLoS One 2021; 16:e0255956. [PMID: 34432825 PMCID: PMC8386827 DOI: 10.1371/journal.pone.0255956] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/27/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Sickle Cell Disease (SCD) is an inherited blood disorder that leads to hemolytic anemia, pain, organ damage and early mortality. It is characterized by polymerized deoxygenated hemoglobin, rigid sickle red blood cells and vaso-occlusive crises (VOC). Recurrent hypoxia-reperfusion injury in the gut of SCD patients could increase tissue injury, permeability, and bacterial translocation. In this context, the gut microbiome, a major player in health and disease, might have significant impact. This study sought to characterize the gut microbiome in SCD. METHODS Stool and saliva samples were collected from healthy controls (n = 14) and SCD subjects (n = 14). Stool samples were also collected from humanized SCD murine models including Berk, Townes and corresponding control mice. Amplified 16S rDNA was used for bacterial composition analysis using Next Generation Sequencing (NGS). Pairwise group analyses established differential bacterial groups at many taxonomy levels. Bacterial group abundance and differentials were established using DeSeq software. RESULTS A major dysbiosis was observed in SCD patients. The Firmicutes/Bacteroidetes ratio was lower in these patients. The following bacterial families were more abundant in SCD patients: Acetobacteraceae, Acidaminococcaceae, Candidatus Saccharibacteria, Peptostreptococcaceae, Bifidobacteriaceae, Veillonellaceae, Actinomycetaceae, Clostridiales, Bacteroidacbactereae and Fusobacteriaceae. This dysbiosis translated into 420 different operational taxonomic units (OTUs). Townes SCD mice also displayed gut microbiome dysbiosis as seen in human SCD. CONCLUSION A major dysbiosis was observed in SCD patients for bacteria that are known strong pro-inflammatory triggers. The Townes mouse showed dysbiosis as well and might serve as a good model to study gut microbiome modulation and its impact on SCD pathophysiology.
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Affiliation(s)
- Hassan Brim
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
| | - James Taylor
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
| | - Muneer Abbas
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
| | - Kimberly Vilmenay
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
| | - Mohammad Daremipouran
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
| | - Sudhir Varma
- Hithru Analytics, Laurel, MD, United States of America
| | - Edward Lee
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
| | - Betty Pace
- University of Augusta, Augusta, GA, United States of America
| | - Waogwende L. Song-Naba
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
| | - Kalpna Gupta
- Division of Hematology, Oncology and Transplantation, Department of Medicine, University of Minnesota, Minneapolis, MN, United States of America
- Hematology/Oncology, Department of Medicine, University of California Irvine, Irvine, CA, United States of America
- Southern California Institute for Research and Education, Long Beach VA Healthcare System, Long Beach, CA, United States of America
| | - Sergei Nekhai
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
| | - Patricia O’Neil
- Food and Drug Administration, Silver Spring, MD, United States of America
| | - Hassan Ashktorab
- Department of Pathology, Department of Medicine, Cancer Center, Microbiology and Center for Sickle Cell Disease, Howard University College of Medicine, Washington, DC, United States of America
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Gu X, Yu T, Guo T, Kong J. A qPCR-based method for rapid quantification of six intestinal homeostasis-relevant bacterial genera in feces. Future Microbiol 2021; 16:895-906. [PMID: 34342236 DOI: 10.2217/fmb-2020-0269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Developing efficient methods for monitoring the complex microbial community to rapidly assess the health status. Materials & methods: The qPCR-based method was developed, verified and in situ applied in fecal samples. Results: Six primer pairs with high specificity were designed to perform qPCR assays under a unified reaction condition within 2.5 h. The limits of detection, amplification efficiency and feasibility of the qPCR-based method established here were verified. In situ application of 18 fecal samples showed that the amounts of Bacteroides, Streptococcus and Bifidobacterium in colorectal cancer patient feces were obviously lower than those of healthy volunteers. Conclusion: This qPCR-based method was a reliable tool for rapid quantification of the six intestinal homeostasis relevant bacterial genera in feces.
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Affiliation(s)
- Xinyi Gu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Tao Yu
- Qilu Hospital, Shandong University, Jinan, 250012, China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
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Dietary supplementation of Bacillus subtilis PB6 improves sow reproductive performance and reduces piglet birth intervals. ACTA ACUST UNITED AC 2020; 6:278-287. [PMID: 33005761 PMCID: PMC7503085 DOI: 10.1016/j.aninu.2020.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/31/2020] [Accepted: 04/03/2020] [Indexed: 01/15/2023]
Abstract
We investigated the effects of dietary supplementation with Bacillus subtilis PB6 (B. subtilis PB6) during late gestation and lactation on sow reproductive performance, antioxidant indices, and gut microbiota. A total of 32 healthy Landrace × Yorkshire sows on d 90 of gestation were randomly assigned to 2 groups, with 16 replicates per group, receiving basal diet (CON) or the basal diet + 0.2% B. subtilis PB6, containing 4.0 × 108 CFU/kg of feed (BS). The litter sizes (total born) and numbers of piglets born alive were larger in the BS group (P < 0.01), whereas the weights of piglets born alive and the piglet birth intervals were lower in the BS group (P < 0.05). Although the litter weights and piglet bodyweights (after cross-fostering) were lower after BS treatment (P < 0.05), the litter sizes, litter weights, lactation survival rate, and litter weight gains at weaning were higher in BS group (P < 0.05). The concentrations of malondialdehyde (MDA) in the sow sera at parturition were lower in the BS group (P < 0.01). The serum total antioxidant capacity (T-AOC) at parturition and the serum catalase (CAT) concentrations on d 21 of lactation were higher in the BS group (P < 0.05). Dietary supplementation with B. subtilis PB6 (P < 0.05) reduced the serum endotoxin concentrations in the sows and the serum cortisol concentrations of the piglets at d 14 of lactation. The α-diversity indices of microbial were higher in the CON group (P < 0.05). At the phylum level, B. subtilis PB6 supplementation increased the relative abundances of Gemmatimonadete and Acidobacteria (both P < 0.01) and reduced those of Proteobacteria, and Actinobacteria (both P < 0.05). At the genus level, B. subtilis PB6 supplementation increased the relative abundance of Ruminococcaceae_UCG-013 cc (P < 0.05) and reduced that of Streptococcus (P < 0.05). This study demonstrated that adding 4.0 × 108 CFU/kg B. subtilis PB6 to sows' feed during late gestation and lactation could shorten piglet birth intervals, enhance the growth performance of suckling piglets, and improve the gut health of sows during late gestation.
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Cao M, Li Y, Wu QJ, Zhang P, Li WT, Mao ZY, Wu DM, Jiang XM, Zhuo Y, Fang ZF, Che LQ, Xu SY, Feng B, Li J, Lin Y, Wu D. Effects of dietary Clostridium butyricum addition to sows in late gestation and lactation on reproductive performance and intestinal microbiota1. J Anim Sci 2019; 97:3426-3439. [PMID: 31233597 DOI: 10.1093/jas/skz186] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/17/2019] [Indexed: 12/24/2022] Open
Abstract
This study was conducted to investigate the effects of Clostridium butyricum addition to diets in late gestation and lactation on the reproductive performance and gut microbiota for sows. A total of 180 healthy Landrace × Yorkshire sows at 90 d of gestation were randomly assigned to one of four groups, with 45 replicates per group, receiving a basal commercial diet (Control, 0% C. butyricum) or diet added with 0.1% C. butyricum (1 × 108 CFU/kg of feed), 0.2% C. butyricum (2 × 108 CFU/kg of feed), 0.4% C. butyricum (4 × 108 CFU/kg of feed), respectively. The experiment was conducted from 90 d of gestation to weaning at 21 d of lactation. The results showed that the interval between piglet born was linearly (P < 0.05) decreased, and the duration of farrowing was significantly (quadratic, P < 0.05) shortened as C. butyricum addition increased. There was a linear (P < 0.05) increase in litter weight at weaning and litter weight gain. The concentrations of IgG and IgM in colostrum, and IgM in milk were linearly increased (P < 0.05) as C. butyricum addition. Serum MDA concentrations of sows at parturition and 14 d in lactation, and piglets at 14 and 21 d of age were linearly (P < 0.05) decreased, respectively. The serum total antioxidant capacity concentrations of sows at parturition and 14 and 21 d in lactation, and piglets at 14 and 21 d of age were linearly (P < 0.05) increased as C. butyricum addition, respectively. There was a linear decrease in the serum endotoxin concentration of sows on 21 d in lactation (P < 0.05). The serum cortisol concentrations of piglets at 14 and 21 d of age were both significantly (quadratic, P < 0.05) decreased. The 0.2% C. butyricum increased the relative abundance of Bacteroidetes (P = 0.016) at phylum level, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotellaceae_UCG-003, Prevotella_9, Alloprevotella (P < 0.05) at genus level, and decreased the relative abundance of Proteobacteria, Gemmatimonadetes, Actinobacteria (P < 0.001) at phylum level, and Clostridium_sensu_stricto_1, Streptococcus, Escheruchia-Shigella, Sphingomonas, Succinivibrio (P < 0.05) at genus level and Firmicutes/Bacteroidetes ratio (P = 0.020). In conclusion, the present research indicated that dietary addition with C. butyricum could shorten the duration of farrowing and enhance the growth performance of suckling piglets. Moreover, 0.2% C. butyricum administration to sows changed the composition of intestinal microbiota, especially increased the relative abundance of Prevotella.
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Affiliation(s)
- Meng Cao
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiujie J Wu
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Pan Zhang
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Wentao T Li
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhengyu Y Mao
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Dongmei M Wu
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Xuemei M Jiang
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yong Zhuo
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhengfeng F Fang
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Lianqiang Q Che
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Shengyu Y Xu
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Bin Feng
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Li
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - Yan Lin
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
| | - De Wu
- Key Laboratory for Animal Disease Resistance Nutrition of the Ministry of Education of China, Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, China
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Hamidi B, Wallace K, Vasu C, Alekseyenko AV. W ∗d -test: robust distance-based multivariate analysis of variance. MICROBIOME 2019; 7:51. [PMID: 30935409 PMCID: PMC6444669 DOI: 10.1186/s40168-019-0659-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/11/2019] [Indexed: 05/15/2023]
Abstract
BACKGROUND Community-wide analyses provide an essential means for evaluation of the effect of interventions or design variables on the composition of the microbiome. Applications of these analyses are omnipresent in microbiome literature, yet some of their statistical properties have not been tested for robustness towards common features of microbiome data. Recently, it has been reported that PERMANOVA can yield wrong results in the presence of heteroscedasticity and unbalanced sample sizes. FINDINGS We develop a method for multivariate analysis of variance, [Formula: see text], based on Welch MANOVA that is robust to heteroscedasticity in the data. We do so by extending a previously reported method that does the same for two-level independent factor variables. Our approach can accommodate multi-level factors, stratification, and multiple post hoc testing scenarios. An R language implementation of the method is available at https://github.com/alekseyenko/WdStar . CONCLUSION Our method resolves potential for confounding of location and dispersion effects in multivariate analyses by explicitly accounting for the differences in multivariate dispersion in the data tested. The methods based on [Formula: see text] have general applicability in microbiome and other 'omics data analyses.
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Affiliation(s)
- Bashir Hamidi
- Program for Human Microbiome Research, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA
- Biomedical Informatics Center, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA
| | - Kristin Wallace
- Department of Public Health Science, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA
| | - Chenthamarakshan Vasu
- Department of Microbiology and Immunology, Medical University of South Carolina, 173 Ashley Avenue MSC 509, Charleston, 29425, SC, USA
| | - Alexander V Alekseyenko
- Program for Human Microbiome Research, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA.
- Biomedical Informatics Center, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA.
- Department of Public Health Science, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA.
- Department of Oral Health Sciences, Medical University of South Carolina, 135 Cannon Street MSC 200, Charleston, 29425, SC, USA.
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Deciphering the Colorectal Cancer Gut Microbiota: Association vs. Causality. CURRENT COLORECTAL CANCER REPORTS 2019. [DOI: 10.1007/s11888-019-00431-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Bridges KM, Diaz FJ, Wang Z, Ahmed I, Sullivan DK, Umar S, Buckles DC, Greiner KA, Hester CM. Relating Stool Microbial Metabolite Levels, Inflammatory Markers and Dietary Behaviors to Screening Colonoscopy Findings in a Racially/Ethnically Diverse Patient Population. Genes (Basel) 2018; 9:genes9030119. [PMID: 29495356 PMCID: PMC5867840 DOI: 10.3390/genes9030119] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/09/2018] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is the third leading cause of cancer death for both men and women in the United States, yet it is treatable and preventable. African Americans have higher incidence of CRC than other racial/ethnic groups, however, it is unclear whether this disparity is primarily due to environmental or biological factors. Short chain fatty acids (SCFAs) are metabolites produced by bacteria in the colon and are known to be inversely related to CRC progression. The aim of this study is to investigate how stool SCFA levels, markers of inflammation in stool and dietary intake relate to colonoscopy findings in a diverse patient population. Stool samples from forty-eight participants were analyzed for SCFA levels and inflammatory markers (lysozyme, secretory IgA, lactoferrin). Additionally, participants completed the National Cancer Institute's Diet History Questionnaire II (DHQ II) to report dietary intake over the past year. Subsequently, the majority of participants underwent screening colonoscopy. Our results showed that African Americans had higher total levels of SCFAs in stool than other racial/ethnic groups, significantly lower intake of non-starchy vegetables and similar inflammatory marker expression and colonoscopy outcomes, compared to others. This work is an initial exploration into the biological and clinical factors that may ultimately inform personalized screening approaches and clinical decision-making to improve colorectal cancer disparities for African Americans.
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Affiliation(s)
- Kristina M Bridges
- Department of Family Medicine Research Division, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Francisco J Diaz
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Zhiwen Wang
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Ishfaq Ahmed
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Debra K Sullivan
- Department of Dietetics and Nutrition, University of Kansas Medical Center, Kansas City, KS 66160, USA.
- University of Kansas Cancer Center, Kansas City, KS 66160, USA.
| | - Shahid Umar
- Department of Surgery, University of Kansas Medical Center, Kansas City, KS 66160, USA.
- University of Kansas Cancer Center, Kansas City, KS 66160, USA.
| | - Daniel C Buckles
- Department of Internal Medicine, Gastroenterology and Hepatology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - K Allen Greiner
- Department of Family Medicine Research Division, University of Kansas Medical Center, Kansas City, KS 66160, USA.
- University of Kansas Cancer Center, Kansas City, KS 66160, USA.
| | - Christina M Hester
- Department of Family Medicine Research Division, University of Kansas Medical Center, Kansas City, KS 66160, USA.
- University of Kansas Cancer Center, Kansas City, KS 66160, USA.
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