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Mahdavi M, Prévost K, Balthazar P, Hus IFP, Duchesne É, Dumont N, Gagné-Ouellet V, Gagnon C, Laforest-Lapointe I, Massé E. Disturbance of the human gut microbiota in patients with Myotonic Dystrophy type 1. Comput Struct Biotechnol J 2024; 23:2097-2108. [PMID: 38803516 PMCID: PMC11128782 DOI: 10.1016/j.csbj.2024.05.009] [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: 11/13/2023] [Revised: 04/29/2024] [Accepted: 05/06/2024] [Indexed: 05/29/2024] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a rare autosomal dominant genetic disorder. Although DM1 is primarily characterized by progressive muscular weakness, it exhibits many multisystemic manifestations, such as cognitive deficits, cardiac conduction abnormalities, and cataracts, as well as endocrine and reproductive issues. Additionally, the gastrointestinal (GI) tract is frequently affected, encompassing the entire digestive tract. However, the underlying causes of these GI symptoms remain uncertain, whether it is biomechanical problems of the intestine, involvement of bacterial communities, or both. The primary objective of this study is to investigate the structural changes in the gut microbiome of DM1 patients. To achieve this purpose, 35 patients with DM1 were recruited from the DM-Scope registry of the neuromuscular clinic in the Saguenay-Lac-St-Jean region of the province of Québec, Canada. Stool samples from these 35 patients, including 15 paired samples with family members living with them as controls, were collected. Subsequently, these samples were sequenced by 16S MiSeq and were analyzed with DADA2 to generate taxonomic signatures. Our analysis revealed that the DM1 status correlated with changes in gut bacterial community. Notably, there were differences in the relative abundance of Bacteroidota, Euryarchaeota, Fusobacteriota, and Cyanobacteria Phyla compared to healthy controls. However, no significant shift in gut microbiome community structure was observed between DM1 phenotypes. These findings provide valuable insights into how the gut bacterial community, in conjunction with biomechanical factors, could potentially influence the gastrointestinal tract of DM1 patients.
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Affiliation(s)
- Manijeh Mahdavi
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Karine Prévost
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Philippe Balthazar
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Isabelle Fisette-Paul Hus
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Élise Duchesne
- Physiotherapy teaching unit, Université du Québec à Chicoutimi, Chicoutimi, G7H 2B1, Canada
| | - Nicolas Dumont
- School of Rehabilitation, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Valérie Gagné-Ouellet
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Cynthia Gagnon
- Department of Rehabilitation, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | | | - Eric Massé
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, QC J1E 4K8, Canada
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Zhang L, Vaccari F, Bandini F, Puglisi E, Trevisan M, Lucini L. The short-term effect of microplastics in lettuce involves size- and dose-dependent coordinate shaping of root metabolome, exudation profile and rhizomicrobiome. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 945:174001. [PMID: 38879040 DOI: 10.1016/j.scitotenv.2024.174001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 06/02/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Micro- and nano-plastics (MNPs) in the soil can impact the microbial diversity within rhizospheres and induce modifications in plants' morphological, physiological, and biochemical parameters. However, a significant knowledge gap still needs to be addressed regarding the specific effects of varying particle sizes and concentrations on the comprehensive interplay among soil dynamics, root exudation, and the overall plant system. In this sense, different omics techniques were employed to clarify the mechanisms of the action exerted by four different particle sizes of polyethylene plastics considering four different concentrations on the soil-roots exudates-plant system was studied using lettuce (Lactuca sativa L. var. capitata) as a model plant. The impact of MNPs was investigated using a multi-omics integrated approach, focusing on the tripartite interaction between the root metabolic process, exudation pattern, and rhizosphere microbial modulation. Our results showed that particle size and their concentrations significantly modulated the soil-roots exudates-plant system. Untargeted metabolomics highlighted that fatty acids, amino acids, and hormone biosynthesis pathways were significantly affected by MNPs. Additionally, they were associated with the reduction of rhizosphere bacterial α-diversity, following a size-dependent trend for specific taxa. The omics data integration highlighted a correlation between Pseudomonadata and Actinomycetota phyla and Bacillaceae family (Peribacillus simplex) and the exudation of flavonoids, phenolic acids, and lignans in lettuce exposed to increasing sizes of MNPs. This study provides a novel insight into the potential effects of different particle sizes and concentrations of MNPs on the soil-plant continuum, providing evidence about size- and concentration-dependent effects, suggesting the need for further investigation focused on medium- to long-term exposure.
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Affiliation(s)
- Leilei Zhang
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Filippo Vaccari
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Francesca Bandini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Edoardo Puglisi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Marco Trevisan
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Luigi Lucini
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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Barron M, Fernando DG, Atkinson SN, Kirby J, Kindel TL. Sleeve Gastrectomy Protects Against Hypertension in Rats due to Changes in the Gut Microbiome. J Surg Res 2024; 301:118-126. [PMID: 38925098 DOI: 10.1016/j.jss.2024.05.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 04/26/2024] [Accepted: 05/11/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION Sleeve gastrectomy (SG), results in improvement in hypertension. We have previously published that rodent SG improves hypertension independent of weight loss associated with unique shifts in the gut microbiome. We tested if the gut microbiome directly improves blood pressure by performing fecal material transfer (FMT) from post-SG rats to surgery-naïve animals. METHODS We performed SG or Sham surgery in male, Zucker rats (n = 6-7) with obesity. Stool was collected postop from surgical donors for treatment of recipient rats. Three nonsurgical groups received daily, oral consumption of SG stool, sham stool, or vehicle alone (Nutella) for 10 wk (n = 7-8). FMT treatment was assessed for effects on body weight, food intake, oral glucose tolerance, and blood pressure. Genomic deoxyribonucleic acid of stool from donor and recipient groups were sequenced by 16S ribosomal ribonucleic acid and analyzed for diversity, abundance, and importance. RESULTS Ten weeks of SG-FMT treatment significantly lowered systolic blood pressures in surgery-naïve, recipient rats compared to vehicle treatment alone (126.8 ± 13.3 mmHg versus 151.8 ± 12.2 mmHg, P = 0.001). SG-FMT treatment also significantly altered beta diversity metrics compared to Sham-FMT and vehicle treatment. In random forest analysis, amplicon sequence variant level significantly predicted FMT group, P = 0.01. CONCLUSIONS We have found a direct link between gut microbial changes after SG and regulation of blood pressure. Future mechanistic studies are required to learn what specific gut microbial changes are required to induce improvements in obesity-associated hypertension and translation to clinical, metabolic surgery.
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Affiliation(s)
| | | | - Samantha N Atkinson
- Department of Microbiology and Immunology, Milwaukee, Wisconsin; Center for Microbiome Research, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - John Kirby
- Department of Microbiology and Immunology, Milwaukee, Wisconsin
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4
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Berrios L, Bogar GD, Bogar LM, Venturini AM, Willing CE, Del Rio A, Ansell TB, Zemaitis K, Velickovic M, Velickovic D, Pellitier PT, Yeam J, Hutchinson C, Bloodsworth K, Lipton MS, Peay KG. Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities. mSystems 2024; 9:e0036924. [PMID: 38717159 DOI: 10.1128/msystems.00369-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 04/11/2024] [Indexed: 06/19/2024] Open
Abstract
Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.
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Affiliation(s)
- Louis Berrios
- Department of Biology, Stanford University, Stanford, California, USA
| | - Glade D Bogar
- Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Laura M Bogar
- Department of Plant Biology, University of California, Davis, Davis, California, USA
| | | | - Claire E Willing
- Department of Biology, Stanford University, Stanford, California, USA
- School of Environmental and Forest Sciences, University of Washington, Seattle, Washington, USA
| | - Anastacia Del Rio
- Department of Biology, Stanford University, Stanford, California, USA
| | - T Bertie Ansell
- Department of Biology, Stanford University, Stanford, California, USA
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Kevin Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Marija Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Dusan Velickovic
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Peter T Pellitier
- Department of Biology, Stanford University, Stanford, California, USA
| | - Jay Yeam
- Department of Biology, Stanford University, Stanford, California, USA
| | - Chelsea Hutchinson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kent Bloodsworth
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Mary S Lipton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Kabir G Peay
- Department of Biology, Stanford University, Stanford, California, USA
- Department of Earth System Science, Stanford University, Stanford, California, USA
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Hong D, Kim HK, Yang W, Yoon C, Kim M, Yang CS, Yoon S. Integrative analysis of single-cell RNA-seq and gut microbiome metabarcoding data elucidates macrophage dysfunction in mice with DSS-induced ulcerative colitis. Commun Biol 2024; 7:731. [PMID: 38879692 PMCID: PMC11180211 DOI: 10.1038/s42003-024-06409-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 06/03/2024] [Indexed: 06/19/2024] Open
Abstract
Ulcerative colitis (UC) is a significant inflammatory bowel disease caused by an abnormal immune response to gut microbes. However, there are still gaps in our understanding of how immune and metabolic changes specifically contribute to this disease. Our research aims to address this gap by examining mouse colons after inducing ulcerative colitis-like symptoms. Employing single-cell RNA-seq and 16 s rRNA amplicon sequencing to analyze distinct cell clusters and microbiomes in the mouse colon at different time points after induction with dextran sodium sulfate. We observe a significant reduction in epithelial populations during acute colitis, indicating tissue damage, with a partial recovery observed in chronic inflammation. Analyses of cell-cell interactions demonstrate shifts in networking patterns among different cell types during disease progression. Notably, macrophage phenotypes exhibit diversity, with a pronounced polarization towards the pro-inflammatory M1 phenotype in chronic conditions, suggesting the role of macrophage heterogeneity in disease severity. Increased expression of Nampt and NOX2 complex subunits in chronic UC macrophages contributes to the inflammatory processes. The chronic UC microbiome exhibits reduced taxonomic diversity compared to healthy conditions and acute UC. The study also highlights the role of T cell differentiation in the context of dysbiosis and its implications in colitis progression, emphasizing the need for targeted interventions to modulate the inflammatory response and immune balance in colitis.
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MESH Headings
- Animals
- Colitis, Ulcerative/microbiology
- Colitis, Ulcerative/immunology
- Colitis, Ulcerative/genetics
- Colitis, Ulcerative/chemically induced
- Colitis, Ulcerative/pathology
- Gastrointestinal Microbiome
- Macrophages/immunology
- Macrophages/microbiology
- Macrophages/metabolism
- Dextran Sulfate/toxicity
- Dextran Sulfate/adverse effects
- Mice
- Single-Cell Analysis
- RNA-Seq
- Mice, Inbred C57BL
- Disease Models, Animal
- DNA Barcoding, Taxonomic
- RNA, Ribosomal, 16S/genetics
- Male
- Single-Cell Gene Expression Analysis
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Affiliation(s)
- Dawon Hong
- RNA Cell Biology Laboratory, Graduate Department of Bioconvergence Engineering, Dankook University, Yongin, Republic of Korea
| | - Hyo Keun Kim
- Dept of Molecular and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, Korea
| | - Wonhee Yang
- Department of AI-based Convergence, Dankook University, Yongin, Republic of Korea
| | - Chanjin Yoon
- Dept of Molecular and Life Science and Institute of Natural Science and Technology, Hanyang University, Ansan-si, Korea
| | - Minsoo Kim
- Department of Computer Science, College of SW Convergence, Dankook University, Yongin, Republic of Korea
| | - Chul-Su Yang
- Dept of Medicinal and Life Science and Center for Bionano Intelligence Education and Research, Hanyang University, Ansan-si, Korea.
| | - Seokhyun Yoon
- Department of Electronics & Electrical Engineering, College of Engineering, Dankook University, Yongin, Republic of Korea.
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Flores-Vargas G, Bergsveinson J, Korber DR. Environmentally Relevant Antibiotic Concentrations Exert Stronger Selection Pressure on River Biofilm Resistomes than AMR-Reservoir Effluents. Antibiotics (Basel) 2024; 13:539. [PMID: 38927205 PMCID: PMC11200958 DOI: 10.3390/antibiotics13060539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Freshwater environments are primary receiving systems of wastewater and effluents, which carry low concentrations of antibiotics and antimicrobial-resistant (AMR) bacteria and genes. Aquatic microbial communities are thus exposed to environmentally relevant concentrations of antibiotics (ERCA) that presumably influence the acquisition and spread of environmental AMR. Here, we analyzed ERCA exposure with and without the additional presence of municipal wastewater treatment plant effluent (W) and swine manure run-off (M) on aquatic biofilm resistomes. Microscopic analyses revealed decreased taxonomic diversity and biofilm structural integrity, while metagenomic analysis revealed an increased abundance of resistance, virulence, and mobile element-related genes at the highest ERCA exposure levels, with less notable impacts observed when solely exposed to W or M effluents. Microbial function predictions indicated increased gene abundance associated with energy and cell membrane metabolism and heavy metal resistance under ERCA conditions. In silico predictions of increased resistance mechanisms did not correlate with observed phenotypic resistance patterns when whole communities were exposed to antimicrobial susceptibility testing. This reveals important insight into the complexity of whole-community coordination of physical and genetic responses to selective pressures. Lastly, the environmental AMR risk assessment of metagenomic data revealed a higher risk score for biofilms grown at sub-MIC antibiotic conditions.
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Affiliation(s)
- Gabriela Flores-Vargas
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
| | - Jordyn Bergsveinson
- Environment and Climate Change Canada, 11 Innovation Blvd., Saskatoon, SK S7N 3H5, Canada;
| | - Darren R. Korber
- Food and Bioproduct Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada;
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Zhou X, Liu H, Fan X, Wang X, Bi X, Cheng L, Huang S, Zhao F, Yang T. Comparative Analysis of Bacterial Information of Biofilms and Activated Sludge in Full-Scale MBBR-IFAS Systems. Microorganisms 2024; 12:1121. [PMID: 38930504 PMCID: PMC11206091 DOI: 10.3390/microorganisms12061121] [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] [Received: 04/09/2024] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
This study extensively analyzed the bacterial information of biofilms and activated sludge in oxic reactors of full-scale moving bed biofilm reactor-integrated fixed-film activated sludge (MBBR-IFAS) systems. The bacterial communities of biofilms and activated sludge differed statistically (R = 0.624, p < 0.01). The denitrifying genera Ignavibacterium, Phaeodactylibacter, Terrimonas, and Arcobacter were more abundant in activated sludge (p < 0.05), while comammox Nitrospira was more abundant in biofilms (p < 0.05), with an average relative abundance of 8.13%. Nitrospira and Nitrosomonas had weak co-occurrence relationships with other genera in the MBBR-IFAS systems. Potential function analysis revealed no differences in pathways at levels 1 and 2 based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) between biofilms and activated sludge. However, in terms of pathways at level 3, biofilms had more potential in 26 pathways, including various organic biodegradation and membrane and signal transportation pathways. In comparison, activated sludge had more potential in only five pathways, including glycan biosynthesis and metabolism. With respect to nitrogen metabolism, biofilms had greater potential for nitrification (ammonia oxidation) (M00528), and complete nitrification (comammox) (M00804) concretely accounted for methane/ammonia monooxygenase (K10944, K10945, and K10946) and hydroxylamine dehydrogenase (K10535). This study provides a theoretical basis for MBBR-IFAS systems from the perspective of microorganisms.
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Affiliation(s)
| | | | - Xing Fan
- State and Local Joint Engineering Research Centre of Urban Wastewater Treatment and Reclamation, Qingdao University of Technology, Qingdao 266520, China (F.Z.); (T.Y.)
| | | | - Xuejun Bi
- State and Local Joint Engineering Research Centre of Urban Wastewater Treatment and Reclamation, Qingdao University of Technology, Qingdao 266520, China (F.Z.); (T.Y.)
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Hernandez AR, Parker E, Babar M, Banerjee A, Ding S, Simley A, Buford TW. Microbiome-driven alterations in metabolic pathways and impaired cognition in aged female TgF344-AD rats. AGING BRAIN 2024; 5:100119. [PMID: 38881651 PMCID: PMC11179252 DOI: 10.1016/j.nbas.2024.100119] [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: 01/15/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 06/18/2024] Open
Abstract
Alzheimer's disease (AD) not only affects cognition and neuropathology, but several other facets capable of negatively impacting quality of life and potentially driving impairments, including altered gut microbiome (GMB) composition and metabolism. Aged (20 + mo) female TgF344-AD and wildtype rats were cognitively characterized on several tasks incorporating several cognitive domains, including task acquisition, object recognition memory, anxiety-like behaviors, and spatial navigation. Additionally, metabolic phenotyping, GMB sequencing throughout the intestinal tract (duodenum, jejunum, ileum, colon, and feces), neuropathological burden assessment and marker gene functional abundance predictions (PICRUSt2) were conducted. TgF344-AD rats demonstrated significant cognitive impairment in multiple domains, as well as regionally specific GMB dysbiosis. Relationships between peripheral factors were investigated using Canonical Correspondence Analysis (CCA), revealing correlations between GMB changes and both cognitive and metabolic factors. Moreover, communities of gut microbes contributing to essential metabolic pathways were significantly altered in TgF344-AD rats. These data indicate dysbiosis may affect cognitive outcomes in AD through alterations in metabolism-related enzymatic pathways that are necessary for proper brain function. Moreover, these changes were mostly observed in intestinal segments required for carbohydrate digestion, not fecal samples. These data support the targeting of intestinal and microbiome health for the treatment of AD.
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Affiliation(s)
- Abbi R Hernandez
- Department of Medicine, Division of Geriatrics, Gerontology & Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Erik Parker
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University-Bloomington, Bloomington, IN 47405, USA
| | - Maham Babar
- Department of Medicine, Division of Geriatrics, Gerontology & Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Anisha Banerjee
- Department of Medicine, Division of Geriatrics, Gerontology & Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Sarah Ding
- Department of Medicine, Division of Geriatrics, Gerontology & Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Alexis Simley
- Department of Medicine, Division of Geriatrics, Gerontology & Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
| | - Thomas W Buford
- Department of Medicine, Division of Geriatrics, Gerontology & Palliative Care, University of Alabama at Birmingham, Birmingham, AL 35205, USA
- Birmingham/Atlanta VA GRECC, Birmingham VA Medical Center, Birmingham, AL 35244, USA
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9
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Rosas-Campos R, Sandoval-Rodríguez AS, Rodríguez-Sanabria JS, Vazquéz-Esqueda ÁO, Alfaro-Martinez CR, Escutia-Gutiérrez R, Vega-Magaña N, Peña-Rodríguez M, Zepeda-Nuño JS, Andrade-Marcial M, Campos-Uscanga Y, Jave-Suárez LF, Santos A, Cerda-Reyes E, Almeida-López M, Martínez-López E, Herrera LA, Armendariz-Borunda J. A Novel Foodstuff Mixture Improves the Gut-Liver Axis in MASLD Mice and the Gut Microbiota in Overweight/Obese Patients. Antioxidants (Basel) 2024; 13:664. [PMID: 38929103 PMCID: PMC11200377 DOI: 10.3390/antiox13060664] [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] [Received: 05/07/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Microbial community control is crucial for maintaining homeostasis of the gut-liver axis in metabolic dysfunction-associated steatotic liver disease (MASLD). Here, we show that supplementation with a mixture of Mexican foodstuffs (MexMix)-Opuntia ficus indica (nopal), Theobroma cacao (cocoa) and Acheta domesticus (crickets)-enriches several beneficial taxa in MASLD mice and overweight/obese humans. Thus, MexMix induces an important prebiotic effect. In mice, a restoration of intestinal health was observed due to the increased short-chain fatty acids (SCFAs) and intestinal crypt depth, Ocln and Cldn1 expression, and decreased Il6 and Tnfa expression. MexMix significantly reduced steatosis in the mice's liver and modified the expression of 1668 genes. By PCR, we corroborated a Tnfa and Pparg decrease, and a Cat and Sod increase. In addition, MexMix increased the hepatic NRF2 nuclear translocation and miRNA-34a, miRNA-103, and miRNA-33 decline. In overweight/obese humans, MexMix improved the body image satisfaction and reduced the fat intake. These findings indicate that this new food formulation has potential as a therapeutic approach to treat conditions associated with excessive consumption of fats and sugars.
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Affiliation(s)
- Rebeca Rosas-Campos
- Institute for Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico; (R.R.-C.); (A.S.S.-R.); (J.S.R.-S.); (Á.O.V.-E.); (C.R.A.-M.); (R.E.-G.)
| | - Ana Soledad Sandoval-Rodríguez
- Institute for Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico; (R.R.-C.); (A.S.S.-R.); (J.S.R.-S.); (Á.O.V.-E.); (C.R.A.-M.); (R.E.-G.)
| | - Jonathan Samael Rodríguez-Sanabria
- Institute for Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico; (R.R.-C.); (A.S.S.-R.); (J.S.R.-S.); (Á.O.V.-E.); (C.R.A.-M.); (R.E.-G.)
- Departamento Académico de Ciencias Básicas, Universidad Autónoma de Guadalajara, Zapopan 45129, Mexico
| | - Ángel Omar Vazquéz-Esqueda
- Institute for Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico; (R.R.-C.); (A.S.S.-R.); (J.S.R.-S.); (Á.O.V.-E.); (C.R.A.-M.); (R.E.-G.)
| | - Carlos Roberto Alfaro-Martinez
- Institute for Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico; (R.R.-C.); (A.S.S.-R.); (J.S.R.-S.); (Á.O.V.-E.); (C.R.A.-M.); (R.E.-G.)
| | - Rebeca Escutia-Gutiérrez
- Institute for Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico; (R.R.-C.); (A.S.S.-R.); (J.S.R.-S.); (Á.O.V.-E.); (C.R.A.-M.); (R.E.-G.)
| | - Natali Vega-Magaña
- Instituto de Investigación en Ciencias Biomédicas (IICB), Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico;
| | - Marcela Peña-Rodríguez
- Laboratorio de Diagnóstico de Enfermedades Emergentes y Reemergentes (LaDEER), Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico;
| | - José Sergio Zepeda-Nuño
- Centro de Investigación y Diagnóstico de Patología, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico;
| | | | | | - Luis Felipe Jave-Suárez
- División de Inmunología, Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Mexico;
| | - Arturo Santos
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Zapopan 45138, Mexico; (A.S.); (L.A.H.)
| | | | - Mónica Almeida-López
- Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico;
| | - Erika Martínez-López
- Institute of Translational Nutrigenetics and Nutrigenomics, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico;
| | - Luis Alonso Herrera
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Zapopan 45138, Mexico; (A.S.); (L.A.H.)
- Cancer Research Unit, National Institute of Cancerology-Institute of Biomedical Research, National Autonomous University of Mexico (UNAM), Mexico City 70228, Mexico
| | - Juan Armendariz-Borunda
- Institute for Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, Health Sciences University Center, University of Guadalajara, Guadalajara 44340, Mexico; (R.R.-C.); (A.S.S.-R.); (J.S.R.-S.); (Á.O.V.-E.); (C.R.A.-M.); (R.E.-G.)
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Zapopan 45138, Mexico; (A.S.); (L.A.H.)
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10
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Xu J, Knight T, Boone D, Saleem M, Finley SJ, Gauthier N, Ayariga JA, Akinrinlola R, Pulkoski M, Britt K, Tolosa T, Rosado-Rivera YI, Iddrisu I, Thweatt I, Li T, Zebelo S, Burrack H, Thiessen L, Hansen Z, Bernard E, Kuhar T, Samuel-Foo M, Ajayi OS. Influence of Fungicide Application on Rhizosphere Microbiota Structure and Microbial Secreted Enzymes in Diverse Cannabinoid-Rich Hemp Cultivars. Int J Mol Sci 2024; 25:5892. [PMID: 38892079 PMCID: PMC11172691 DOI: 10.3390/ijms25115892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
Microbes and enzymes play essential roles in soil and plant rhizosphere ecosystem functioning. However, fungicides and plant root secretions may impact the diversity and abundance of microbiota structure and enzymatic activities in the plant rhizosphere. In this study, we analyzed soil samples from the rhizosphere of four cannabinoid-rich hemp (Cannabis sativa) cultivars (Otto II, BaOx, Cherry Citrus, and Wife) subjected to three different treatments (natural infection, fungal inoculation, and fungicide treatment). DNA was extracted from the soil samples, 16S rDNA was sequenced, and data were analyzed for diversity and abundance among different fungicide treatments and hemp cultivars. Fungicide treatment significantly impacted the diversity and abundance of the hemp rhizosphere microbiota structure, and it substantially increased the abundance of the phyla Archaea and Rokubacteria. However, the abundances of the phyla Pseudomonadota and Gemmatimonadetes were substantially decreased in treatments with fungicides compared to those without fungicides in the four hemp cultivars. In addition, the diversity and abundance of the rhizosphere microbiota structure were influenced by hemp cultivars. The influence of Cherry Citrus on the diversity and abundance of the hemp rhizosphere microbiota structure was less compared to the other three hemp cultivars (Otto II, BaOx, and Wife). Moreover, fungicide treatment affected enzymatic activities in the hemp rhizosphere. The application of fungicides significantly decreased enzyme abundance in the rhizosphere of all four hemp cultivars. Enzymes such as dehydrogenase, dioxygenase, hydrolase, transferase, oxidase, carboxylase, and peptidase significantly decreased in all the four hemp rhizosphere treated with fungicides compared to those not treated. These enzymes may be involved in the function of metabolizing organic matter and degrading xenobiotics. The ecological significance of these findings lies in the recognition that fungicides impact enzymes, microbiota structure, and the overall ecosystem within the hemp rhizosphere.
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Affiliation(s)
- Junhuan Xu
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
| | - Tyson Knight
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
| | - Donchel Boone
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
| | - Muhammad Saleem
- Department of Biological Sciences, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA
| | - Sheree J. Finley
- Department of Physical and Forensic Sciences, Alabama State University, 915 S. Jackson Street, Montgomery, AL 36104, USA
| | - Nicole Gauthier
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, Lexington, KY 40546, USA;
| | - Joseph A. Ayariga
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
| | - Rufus Akinrinlola
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Melissa Pulkoski
- Department of Crop Science, North Carolina State University, Raleigh, NC 27962, USA
| | - Kadie Britt
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, 220 Price Hall, Blacksburg, VA 24061, USA; (K.B.)
| | - Tigist Tolosa
- Department of Agriculture Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | | | - Ibrahim Iddrisu
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
| | - Ivy Thweatt
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
| | - Ting Li
- Department of Biological Sciences, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA
| | - Simon Zebelo
- Department of Agriculture Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, MD 21853, USA
| | - Hannah Burrack
- Department of Entomology, Michigan State University, East Lansing, MI 48824, USA
| | - Lindsey Thiessen
- Department of Crop Science, North Carolina State University, Raleigh, NC 27962, USA
- USDA-APHIS-PPQ, Raleigh, NC 27606, USA
| | - Zachariah Hansen
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
- Emerging Pests and Pathogens Research Unit, USDA-ARS, 538 Tower Rd., Ithaca, NY 14850, USA
| | - Ernest Bernard
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN 37996, USA
| | - Thomas Kuhar
- Department of Entomology, Virginia Polytechnic Institute and State University, 170 Drillfield Drive, 220 Price Hall, Blacksburg, VA 24061, USA; (K.B.)
| | - Michelle Samuel-Foo
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
| | - Olufemi S. Ajayi
- The Industrial Hemp Program, Alabama State University, 1627 Harris Way, Montgomery, AL 36104, USA (J.A.A.)
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11
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Green GBH, Cox-Holmes AN, Backan O, Valbak O, Potier ACE, Chen D, Morrow CD, Willey CD, McFarland BC. Exploring Gut Microbiota Alterations with Trimethoprim-Sulfamethoxazole and Dexamethasone in a Humanized Microbiome Mouse Model. Microorganisms 2024; 12:1015. [PMID: 38792844 PMCID: PMC11124107 DOI: 10.3390/microorganisms12051015] [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] [Received: 04/16/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Along with the standard therapies for glioblastoma, patients are commonly prescribed trimethoprim-sulfamethoxazole (TMP-SMX) and dexamethasone for preventing infections and reducing cerebral edema, respectively. Because the gut microbiota impacts the efficacy of cancer therapies, it is important to understand how these medications impact the gut microbiota of patients. Using mice that have been colonized with human microbiota, this study sought to examine how TMP-SMX and dexamethasone affect the gut microbiome. Two lines of humanized microbiota (HuM) Rag1-/- mice, HuM1Rag and HuM2Rag, were treated with either TMP-SMX or dexamethasone via oral gavage once a day for a week. Fecal samples were collected pre-treatment (pre-txt), one week after treatment initiation (1 wk post txt), and three weeks post-treatment (3 wk post txt), and bacterial DNA was analyzed using 16S rRNA-sequencing. The HuM1Rag mice treated with TMP-SMX had significant shifts in alpha diversity, beta diversity, and functional pathways at all time points, whereas in the HuM2Rag mice, it resulted in minimal changes in the microbiome. Likewise, dexamethasone treatment resulted in significant changes in the microbiome of the HuM1Rag mice, whereas the microbiome of the HuM2Rag mice was mostly unaffected. The results of our study show that routine medications used during glioblastoma treatment can perturb gut microbiota, with some microbiome compositions being more sensitive than others, and these treatments could potentially affect the overall efficacy of standard-of-care therapy.
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Affiliation(s)
- George B. H. Green
- Department of Cell, Developmental and Integrative Biology, Birmingham, AL 35294, USA
| | - Alexis N. Cox-Holmes
- Department of Cell, Developmental and Integrative Biology, Birmingham, AL 35294, USA
| | - Olivia Backan
- Department of Cell, Developmental and Integrative Biology, Birmingham, AL 35294, USA
- Undergraduate Cancer Biology Program, Birmingham, AL 35294, USA
| | - Olivia Valbak
- Department of Cell, Developmental and Integrative Biology, Birmingham, AL 35294, USA
- Undergraduate Cancer Biology Program, Birmingham, AL 35294, USA
| | - Anna Claire E. Potier
- Department of Cell, Developmental and Integrative Biology, Birmingham, AL 35294, USA
- Undergraduate Cancer Biology Program, Birmingham, AL 35294, USA
| | | | - Casey D. Morrow
- Department of Cell, Developmental and Integrative Biology, Birmingham, AL 35294, USA
| | - Christopher D. Willey
- Department of Radiation Oncology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Braden C. McFarland
- Department of Cell, Developmental and Integrative Biology, Birmingham, AL 35294, USA
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12
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Sall I, Foxall R, Felth L, Maret S, Rosa Z, Gaur A, Calawa J, Pavlik N, Whistler JL, Whistler CA. Gut dysbiosis was inevitable, but tolerance was not: temporal responses of the murine microbiota that maintain its capacity for butyrate production correlate with sustained antinociception to chronic voluntary morphine. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589671. [PMID: 38659831 PMCID: PMC11042308 DOI: 10.1101/2024.04.15.589671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The therapeutic benefits of opioids are compromised by the development of analgesic tolerance, which necessitates higher dosing for pain management thereby increasing the liability for dependence and addiction. Rodent models indicate opposing roles of the gut microbiota in tolerance: morphine-induced gut dysbiosis exacerbates tolerance, whereas probiotics ameliorate tolerance. Not all individuals develop tolerance which could be influenced by differences in microbiota, and yet no study has capitalized upon this natural variation to identify specific features linked to tolerance. We leveraged this natural variation in a murine model of voluntary oral morphine self-administration to elucidate the mechanisms by which microbiota influences tolerance. Although all mice shared similar and predictive morphine-driven microbiota changes that largely masked informative associations with variability in tolerance, our high-resolution temporal analyses revealed a divergence in the progression of dysbiosis that best explained differences in the development in tolerance. Mice that did not develop tolerance also maintained a higher abundance of taxa capable of producing the short-chain fatty acid (SCFA) butyrate, known to bolster intestinal barriers, suppress inflammation, and promote neuronal homeostasis. Furthermore, dietary butyrate supplementation significantly reduced the development of tolerance. These findings could inform immediate therapies to extend the analgesic efficacy of opioids.
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Affiliation(s)
- Izabella Sall
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Graduate program in Molecular and Evolutionary Systems Biology, University of New Hampshire, Durham, NH, USA
| | - Randi Foxall
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Lindsey Felth
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
| | - Soren Maret
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Zachary Rosa
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
| | - Anirudh Gaur
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
| | - Jennifer Calawa
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- Microbiology Graduate Program, University of New Hampshire, Durham, NH, USA
| | - Nadia Pavlik
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Jennifer L. Whistler
- Center for Neuroscience, University of California–Davis, Davis, CA, USA
- Department of Physiology and Membrane Biology, UC Davis School of Medicine, Davis, CA, USA
| | - Cheryl A. Whistler
- Department of Molecular, Cellular, & Biomedical Sciences, University of New Hampshire, Durham, NH, USA
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13
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Yan Z, Lei Y, Zhao P, Zhang D, Shen J, Zhang G, Wei R, Liu H, Liu X, He Y, Shen S, Liu D. Natural mating ability is associated with gut microbiota composition and function in captive male giant pandas. Ecol Evol 2024; 14:e11189. [PMID: 38571808 PMCID: PMC10985376 DOI: 10.1002/ece3.11189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 04/05/2024] Open
Abstract
The issue of poor sexual performance of some male giant pandas seriously impairs the growth and the genetic diversity of the captive population, yet there is still no clear understanding of the cause of the loss of this ability and its underlying mechanism. In this study, we analyzed the gut microbiota and its function in 72 fecal samples obtained from 20 captive male giant pandas, with an equal allocation between individuals capable and incapable of natural mating. Additionally, we investigated fecal hormone levels and behavioral differences between the two groups. A correlation analysis was then conducted among these factors to explore the influencing factors of their natural mating ability. The results showed significant differences in the composition of gut microbiota between the two groups of male pandas. The capable group had significantly higher abundance of Clostridium sensu stricto 1 (p adjusted = .0021, GLMM), which was positively correlated with fatty acid degradation and two-component system functions (Spearman, p adjusted < .05). Additionally, the capable group showed higher gene abundance in gut microbiota function including purine and pyrimidine metabolism and galactose metabolism, as well as pathways related to biological processes such as ribosome and homologous recombination (DEseq2, p adjusted < .05). We found no significant differences in fecal cortisol and testosterone levels between the two groups, and no difference was found in their behavior either. Our study provides a theoretical and practical basis for further studying the behavioral degradation mechanisms of giant pandas and other endangered mammal species.
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Affiliation(s)
- Zheng Yan
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Yinghu Lei
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Pengpeng Zhao
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Danhui Zhang
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Jiena Shen
- Research Center for the Qinling Giant PandaShaanxi Rare Wildlife Rescue BaseXi'anShaanxiChina
| | - Guiquan Zhang
- China Conservation and Research Centre for the Giant PandaWolongSichuanChina
| | - Rongping Wei
- China Conservation and Research Centre for the Giant PandaWolongSichuanChina
| | - Haoqiu Liu
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Xiaoyan Liu
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Yan He
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Sijia Shen
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
| | - Dingzhen Liu
- Department of Ecology, College of Life Sciences, Key Laboratory for Biodiversity and Ecological Engineering of Ministry of EducationBeijing Normal UniversityBeijingHebeiChina
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14
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Wu KC, McCauley KE, Lynch SV, Nayak RR, King NJ, Patel S, Kim TY, Condra K, Fadrosh D, Nguyen D, Lin DL, Lynch K, Rogers SJ, Carter JT, Posselt AM, Stewart L, Schafer AL. Alteration in the gut microbiome is associated with changes in bone metabolism after laparoscopic sleeve gastrectomy. J Bone Miner Res 2024; 39:95-105. [PMID: 38477719 DOI: 10.1093/jbmr/zjad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 11/20/2023] [Accepted: 12/07/2023] [Indexed: 03/14/2024]
Abstract
Laparoscopic sleeve gastrectomy (LSG), the most common bariatric surgical procedure, leads to durable weight loss and improves obesity-related comorbidities. However, it induces abnormalities in bone metabolism. One unexplored potential contributor is the gut microbiome, which influences bone metabolism and is altered after surgery. We characterized the relationship between the gut microbiome and skeletal health in severe obesity and after LSG. In a prospective cohort study, 23 adults with severe obesity underwent skeletal health assessment and stool collection preoperatively and 6 mo after LSG. Gut microbial diversity and composition were characterized using 16S rRNA gene sequencing, and fecal concentrations of short-chain fatty acids (SCFA) were measured with LC-MS/MS. Spearman's correlations and PERMANOVA analyses were applied to assess relationships between the gut microbiome and bone health measures including serum bone turnover markers (C-terminal telopeptide of type 1 collagen [CTx] and procollagen type 1 N-terminal propeptide [P1NP]), areal BMD, intestinal calcium absorption, and calciotropic hormones. Six months after LSG, CTx and P1NP increased (by median 188% and 61%, P < .01) and femoral neck BMD decreased (mean -3.3%, P < .01). Concurrently, there was a decrease in relative abundance of the phylum Firmicutes. Although there were no change in overall microbial diversity or fecal SCFA concentrations after LSG, those with greater within-subject change in gut community microbial composition (β-diversity) postoperatively had greater increases in P1NP level (ρ = 0.48, P = .02) and greater bone loss at the femoral neck (ρ = -0.43, P = .04). In addition, within-participant shifts in microbial richness/evenness (α-diversity) were associated with changes in IGF-1 levels (ρ = 0.56, P < .01). The lower the postoperative fecal butyrate concentration, the lower the IGF-1 level (ρ = 0.43, P = .04). Meanwhile, the larger the decrease in butyrate concentration, the higher the postoperative CTx (ρ = -0.43, P = .04). These findings suggest that LSG-induced gut microbiome alteration may influence skeletal outcomes postoperatively, and microbial influences on butyrate formation and IGF-1 are possible mechanisms.
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Affiliation(s)
- Karin C Wu
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Kathryn E McCauley
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Susan V Lynch
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Renuka R Nayak
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Nicole J King
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Sheena Patel
- California Pacific Medical Center Research Institute, San Francisco, CA 94107, United States
| | - Tiffany Y Kim
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Katherine Condra
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Doug Fadrosh
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Dat Nguyen
- The Campbell Family Institute for Breast Cancer Research, Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Din L Lin
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Kole Lynch
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
| | - Stanley J Rogers
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Jonathan T Carter
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Andrew M Posselt
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
| | - Lygia Stewart
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, United States
- Surgical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
| | - Anne L Schafer
- Department of Medicine, University of California San Francisco, San Francisco, CA 94143, United States
- Medical Services, San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, United States
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, United States
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15
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Yuan H, Wu X, Wang X, Zhou JY, Park S. Microbial Dysbiosis Linked to Metabolic Dysfunction-Associated Fatty Liver Disease in Asians: Prevotella copri Promotes Lipopolysaccharide Biosynthesis and Network Instability in the Prevotella Enterotype. Int J Mol Sci 2024; 25:2183. [PMID: 38396863 PMCID: PMC10889285 DOI: 10.3390/ijms25042183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Metabolic dysfunction-associated fatty liver disease (MAFLD), formerly known as non-alcoholic fatty liver disease (NAFLD), is characterized by hepatic fat accumulation by metabolic dysfunction. The rising prevalence of MAFLD, especially among Asians, may be associated with changes in gut microbiota. We investigated gut microbiota characteristics and potential mechanisms leading to MAFLD development according to enterotypes. Case-control studies examining the gut microbiota composition between MAFLD and non-MAFLD participants were searched in public databases until July 2023. Gut microbiota was categorized into two enterotypes by principal component analysis. According to the enterotypes, LEfSe, ALDEx2, XGBoost, and DCiPatho were utilized to identify differential abundances and pathogenic microbes in the gut between the MAFLD and non-MAFLD groups. We analyzed microbial community networks with the SprCC module and predicted microbial functions. In the Prevotella enterotype (ET-P), 98.6% of Asians and 65.1% of Caucasians were associated with MAFLD (p = 0.049). MAFLD incidence was correlated with enterotype, age, obesity, and ethnicity (p < 0.05). Asian MAFLD patients exhibited decreased Firmicutes and Akkermansia muciniphila and increased Bacteroidetes and P. copri. The pathogenicity scores were 0.006 for A. muciniphila and 0.868 for P. copri. The Asian MAFLD group showed decreased stability and complexity in the gut microbiota network. Metagenome function analysis revealed higher fructose metabolism and lipopolysaccharide (LPS) biosynthesis and lower animal proteins and α-linolenic acid metabolism in Asians with MAFLD compared with the non-MAFLD group. LPS biosynthesis was positively correlated with P. copri (p < 0.05). In conclusion, P. copri emerged as a potential microbial biomarker for MAFLD. These findings enhance our understanding of the pathological mechanisms of MAFLD mediated through the gut microbiota, providing insights for future interventions.
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Affiliation(s)
- Heng Yuan
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Xuangao Wu
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Xichun Wang
- Department of Computer and Data Analysis, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jun-Yu Zhou
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
| | - Sunmin Park
- Department of Bioconvergence, Hoseo University, Asan 31499, Republic of Korea
- Department of Food and Nutrition, Obesity/Diabetes Research Center, Hoseo University, Asan 31499, Republic of Korea
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16
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Fachi JL, Pral LP, Assis HC, Oliveira S, Rodovalho VR, dos Santos JAC, Fernandes MF, Matheus VA, Sesti-Costa R, Basso PJ, Flóro e Silva M, Câmara NOS, Giorgio S, Colonna M, Vinolo MAR. Hyperbaric oxygen augments susceptibility to C. difficile infection by impairing gut microbiota ability to stimulate the HIF-1α-IL-22 axis in ILC3. Gut Microbes 2024; 16:2297872. [PMID: 38165200 PMCID: PMC10763646 DOI: 10.1080/19490976.2023.2297872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
Hyperbaric oxygen (HBO) therapy is a well-established method for improving tissue oxygenation and is typically used for the treatment of various inflammatory conditions, including infectious diseases. However, its effect on the intestinal mucosa, a microenvironment known to be physiologically hypoxic, remains unclear. Here, we demonstrated that daily treatment with hyperbaric oxygen affects gut microbiome composition, worsening antibiotic-induced dysbiosis. Accordingly, HBO-treated mice were more susceptible to Clostridioides difficile infection (CDI), an enteric pathogen highly associated with antibiotic-induced colitis. These observations were closely linked with a decline in the level of microbiota-derived short-chain fatty acids (SCFAs). Butyrate, a SCFA produced primarily by anaerobic microbial species, mitigated HBO-induced susceptibility to CDI and increased epithelial barrier integrity by improving group 3 innate lymphoid cell (ILC3) responses. Mice displaying tissue-specific deletion of HIF-1 in RORγt-positive cells exhibited no protective effect of butyrate during CDI. In contrast, the reinforcement of HIF-1 signaling in RORγt-positive cells through the conditional deletion of VHL mitigated disease outcome, even after HBO therapy. Taken together, we conclude that HBO induces intestinal dysbiosis and impairs the production of SCFAs affecting the HIF-1α-IL-22 axis in ILC3 and worsening the response of mice to subsequent C. difficile infection.
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Affiliation(s)
- José L. Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Laís. P. Pral
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Helder C. Assis
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Sarah Oliveira
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vinícius R. Rodovalho
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Jefferson A. C. dos Santos
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Mariane F. Fernandes
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Valquíria A. Matheus
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Renata Sesti-Costa
- Hematology and Hemotherapy Center, University of Campinas, Campinas, Brazil
| | - Paulo J. Basso
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marina Flóro e Silva
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Niels O. S. Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Selma Giorgio
- Department of Animal Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Marco A. R. Vinolo
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas, Brazil
- Experimental Medicine Research Cluster, Institute of Biology, University of Campinas, Campinas, Brazil
- Obesity and Comorbidities Research Center (OCRC), University of Campinas, Campinas, Brazil
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17
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Popov IV, Popov IV, Krikunova AA, Lipilkina TA, Derezina TN, Chikindas ML, Venema K, Ermakov AM. Gut Microbiota Composition of Insectivorous Synanthropic and Fructivorous Zoo Bats: A Direct Metagenomic Comparison. Int J Mol Sci 2023; 24:17301. [PMID: 38139130 PMCID: PMC10744024 DOI: 10.3390/ijms242417301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Bats are natural reservoirs for many emerging viral diseases. That is why their virome is widely studied. But at the same time, studies of their bacterial gut microbiota are limited, creating a degree of uncertainty about the role of bats in global microbial ecology. In this study, we analyzed gut microbiota of insectivorous Nyctalus noctula and Vespertilio murinus from rehabilitation centers from Rostov-on-Don and Moscow, respectively, and fructivorous Carollia perspicillata from the Moscow Zoo based on V3-V4 16S rRNA metagenomic sequencing. We revealed that microbial diversity significantly differs between the insectivorous and fructivorous species studied, while the differences between N. noctula and V. murinus are less pronounced, which shows that bats' gut microbiota is not strictly species-specific and depends more on diet type. In the gut microbiota of synanthropic bats, we observed bacteria that are important for public health and animal welfare such as Bacteroides, Enterobacter, Clostridiaceae, Enterococcus, Ureaplasma, Faecalibacterium, and Helicobacter, as well as some lactic acid bacteria such as Pediococcus, Lactobacillus, Lactococcus, and Weisella. All these bacteria, except for Bacteroides and Weisella, were significantly less abundant in C. perspicillata. This study provides a direct metagenomic comparison of synanthropic insectivorous and zoo fructivorous bats, suggesting future directions for studying these animals' role in microbial ecology.
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Affiliation(s)
- Igor V. Popov
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
- Division of Immunobiology and Biomedicine, Center of Genetics and Life Sciences, Sirius University of Science and Technology, 354340 Federal Territory Sirius, Russia
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University Campus Venlo, 5928 SZ Venlo, The Netherlands;
| | - Ilia V. Popov
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Anastasya A. Krikunova
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Tatyana A. Lipilkina
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Tatyana N. Derezina
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
| | - Michael L. Chikindas
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
- Health Promoting Naturals Laboratory, School of Environmental and Biological Sciences, Rutgers State University, New Brunswick, NJ 08901, USA
- Department of General Hygiene, I.M. Sechenov First Moscow State Medical University, 119435 Moscow, Russia
| | - Koen Venema
- Centre for Healthy Eating & Food Innovation (HEFI), Maastricht University Campus Venlo, 5928 SZ Venlo, The Netherlands;
| | - Alexey M. Ermakov
- Faculty of Bioengineering and Veterinary Medicine and Center for Agrobiotechnology, Don State Technical University, 344000 Rostov-on-Don, Russia; (I.V.P.); (A.A.K.); (T.A.L.); (T.N.D.); (M.L.C.); (A.M.E.)
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18
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Martinez-Porchas M, Preciado-Álvarez A, Vargas-Albores F, Gracia-Valenzuela MH, Cicala F, Martinez-Cordova LR, Medina-Félix D, Garibay-Valdez E. Microbiota plasticity in tilapia gut revealed by meta-analysis evaluating the effect of probiotics, prebiotics, and biofloc. PeerJ 2023; 11:e16213. [PMID: 37842054 PMCID: PMC10576497 DOI: 10.7717/peerj.16213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 09/10/2023] [Indexed: 10/17/2023] Open
Abstract
Tilapia species are among the most cultivated fish worldwide due to their biological advantages but face several challenges, including environmental impact and disease outbreaks. Feed additives, such as probiotics, prebiotics, and other microorganisms, have emerged as strategies to protect against pathogens and promote immune system activation and other host responses, with consequent reductions in antibiotic use. Because these additives also influence tilapia's gut microbiota and positively affect the tilapia culture, we assume it is a flexible annex organ capable of being subject to significant modifications without affecting the biological performance of the host. Therefore, we evaluated the effect of probiotics and other additives ingested by tilapia on its gut microbiota through a meta-analysis of several bioprojects studying the tilapia gut microbiota exposed to feed additives (probiotic, prebiotic, biofloc). A total of 221 tilapia gut microbiota samples from 14 bioprojects were evaluated. Alpha and beta diversity metrics showed no differentiation patterns in relation to the control group, either comparing additives as a group or individually. Results also revealed a control group with a wide dispersion pattern even when these fish did not receive additives. After concatenating the information, the tilapia gut core microbiota was represented by four enriched phyla including Proteobacteria (31%), Fusobacteria (23%), Actinobacteria (19%), and Firmicutes (16%), and seven minor phyla Planctomycetes (1%), Chlamydiae (1%), Chloroflexi (1%), Cyanobacteria (1%), Spirochaetes (1%), Deinococcus Thermus (1%), and Verrucomicrobia (1%). Finally, results suggest that the tilapia gut microbiota is a dynamic microbial community that can plastically respond to feed additives exposure with the potential to influence its taxonomic profile allowing a considerable optimal range of variation, probably guaranteeing its physiological function under different circumstances.
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Affiliation(s)
- Marcel Martinez-Porchas
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | - Aranza Preciado-Álvarez
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | - Francisco Vargas-Albores
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
| | | | - Francesco Cicala
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Province of Padua, Italy
| | | | - Diana Medina-Félix
- Departamento de Ecología, Universidad Estatal de Sonora, Hermosillo, Sonora, Mexico
| | - Estefania Garibay-Valdez
- Biología de Organismos Acuáticos, Centro de Investigación en Alimentación y Desarrollo, Hermosillo, Sonora, Mexico
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