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Xia X, Lu J, Chen X, Zhou L, Huang Y, Ding S, Li G. Impact of whole grain highland hull-less barley on the denaturing gradient gel electrophoresis profiles of gut microbial communities in rats fed high-fat diets. Microbiol Spectr 2024; 12:e0408923. [PMID: 38747621 DOI: 10.1128/spectrum.04089-23] [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: 12/01/2023] [Accepted: 04/23/2024] [Indexed: 06/06/2024] Open
Abstract
Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) is a traditional non-culture technique that can provide a fingerprint of the microbial community. In the field of gut microbiota analysis, PCR-DGGE still holds potential for development. In the present study, we utilized an improved nested PCR-DGGE approach targeting the V3 region of 16S ribosomal DNA to investigate the impact of whole grain highland hull-less barley (WHLB), a cereal known for its significant hypocholesterolemic effect, on the gut microbiota profiles of high-fat diet rats. Seventy-two male Sprague-Dawley rats were divided into four groups and fed a normal control diet, a high-fat diet, or a high-fat diet supplemented with a low or high dose of WHLB for 4 or 8 weeks. The results revealed that the dominant bands varied among different dose groups and further changed with different treatment times. The compositions of bacterial communities in feces and cecal content were similar, but the dominant bacterial bands differed. After performing double DGGE, extracting the bands, sequencing the DNA, and aligning the sequences, a total of 19 bands were classified under the Firmicutes and Bacteroidetes phyla, while two bands were identified as unclassified uncultured bacteria. The relative abundance of Lactobacillus gasseri, Uncultured Prevotella sp., and Clostridium sp. increased following the administration of WHLB. Illumina-based sequencing was employed to assess the reliability of DGGE, demonstrating its reliability in analyzing the dominant taxonomic composition, although it may have limitations in accurately detecting the alpha diversity of bacterial species. IMPORTANCE While next-generation sequencing has overshadowed polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), the latter still holds promise for advancing gut microbiota analysis due to its unique advantages. In this study, we used optimized nested PCR-DGGE to investigate the gut microbiota profile of high-fat diet rats after administering whole grain highland hull-less barley. High-throughput sequencing was employed to validate the DGGE results. Our results proved the reliability of PCR-DGGE for analyzing the dominant taxonomic composition while also providing visual evidence of a notable relationship between the composition of cecal and fecal microbial communities, highlighting substantial differences in both richness and abundance.
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Affiliation(s)
- Xuejuan Xia
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Jing Lu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Xuanyu Chen
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Lu Zhou
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yadong Huang
- Inner Mongolia Yili Industrial Group Co., Ltd, Hohhot, China
| | - Shunjie Ding
- Army Logistics University of PLA, Chongqing, China
| | - Guannan Li
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Science, Southwest University, Chongqing, China
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Laue HE, Gilmour AJ, Tirado VM, Romano ME. Conceptualizing the Role of the Microbiome as a Mediator and Modifier in Environmental Health Studies: A Scoping Review of Studies of Triclosan and the Microbiome. Curr Environ Health Rep 2024; 11:30-38. [PMID: 38217674 PMCID: PMC10922364 DOI: 10.1007/s40572-024-00428-9] [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] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
PURPOSE OF REVIEW Triclosan is an endocrine-disrupting antimicrobial additive that is suspected of contributing to antibiotic resistance and altering the microbiome. In this scoping review, we summarize what is known about the association between triclosan exposure and the microbiome using evidence from in vivo and epidemiologic studies. RECENT FINDINGS Our review includes 11 rodent studies, seven fish studies, and five human studies. Evidence from animal studies suggests that triclosan decreases the diversity of the microbiome, although only one epidemiologic study agreed. Most studies suggest that triclosan alters the microbial community beta diversity, but disagree on which taxa contributed to compositional differences. Taxa in the Bacteroidetes, Firmicutes, and Proteobacteria may be more influenced by triclosan than those in other phyla. Studies on triclosan and the microbiome were scarce and were inconclusive as to the effects of triclosan on the microbiome. Additional research is needed to clarify windows of heightened susceptibility of the microbiome to triclosan. We recommend guidelines for future microbiome research in environmental health to increase comparability across studies.
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Affiliation(s)
- Hannah E Laue
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA.
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, One Medical Center Dr, WTRB 700 HB 7927, Lebanon, NH, 03756, USA.
| | - Aislinn J Gilmour
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
| | | | - Megan E Romano
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Hanover, NH, USA
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Chen X, Hou Y, Liao A, Pan L, Yang S, Liu Y, Wang J, Xue Y, Zhang M, Zhu Z, Huang J. Integrated Analysis of Gut Microbiome and Adipose Transcriptome Reveals Beneficial Effects of Resistant Dextrin from Wheat Starch on Insulin Resistance in Kunming Mice. Biomolecules 2024; 14:186. [PMID: 38397423 PMCID: PMC10886926 DOI: 10.3390/biom14020186] [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: 12/03/2023] [Revised: 01/14/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
Systemic chronic inflammation is recognized as a significant contributor to the development of obesity-related insulin resistance. Previous studies have revealed the physiological benefits of resistant dextrin (RD), including obesity reduction, lower fasting glucose levels, and anti-inflammation. The present study investigated the effects of RD intervention on insulin resistance (IR) in Kunming mice, expounding the mechanisms through the gut microbiome and transcriptome of white adipose. In this eight-week study, we investigated changes in tissue weight, glucose-lipid metabolism levels, serum inflammation levels, and lesions of epididymal white adipose tissue (eWAT) evaluated via Hematoxylin and Eosin (H&E) staining. Moreover, we analyzed the gut microbiota composition and transcriptome of eWAT to assess the potential protective effects of RD intervention. Compared with a high-fat, high-sugar diet (HFHSD) group, the RD intervention significantly enhanced glucose homeostasis (e.g., AUC-OGTT, HOMA-IR, p < 0.001), and reduced lipid metabolism (e.g., TG, LDL-C, p < 0.001) and serum inflammation levels (e.g., IL-1β, IL-6, p < 0.001). The RD intervention also led to changes in the gut microbiota composition, with an increase in the abundance of probiotics (e.g., Parabacteroides, Faecalibaculum, and Muribaculum, p < 0.05) and a decrease in harmful bacteria (Colidextribacter, p < 0.05). Moreover, the RD intervention had a noticeable effect on the gene transcription profile of eWAT, and KEGG enrichment analysis revealed that differential genes were enriched in PI3K/AKT, AMPK, in glucose-lipid metabolism, and in the regulation of lipolysis in adipocytes signaling pathways. The findings demonstrated that RD not only ameliorated IR, but also remodeled the gut microbiota and modified the transcriptome profile of eWAT.
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Affiliation(s)
- Xinyang Chen
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yinchen Hou
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Aimei Liao
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Long Pan
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Shengru Yang
- College of Food and Biological Engineering, Henan University of Animal Husbandry and Economy, Zhengzhou 450046, China;
| | - Yingying Liu
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jingjing Wang
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Yingchun Xue
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Mingyi Zhang
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Zhitong Zhu
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Jihong Huang
- Food Laboratory of Zhongyuan, Luohe 462300, China; (X.C.); (Y.H.); (A.L.); (L.P.); (Y.L.); (J.W.); (Y.X.); (M.Z.); (Z.Z.)
- School of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng 475004, China
- School of Food and Pharmacy, Xuchang University, Xuchang 461000, China
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Duffy EP, Bachtell RK, Ehringer MA. Opioid trail: Tracking contributions to opioid use disorder from host genetics to the gut microbiome. Neurosci Biobehav Rev 2024; 156:105487. [PMID: 38040073 PMCID: PMC10836641 DOI: 10.1016/j.neubiorev.2023.105487] [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: 08/29/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/03/2023]
Abstract
Opioid use disorder (OUD) is a worldwide public health crisis with few effective treatment options. Traditional genetics and neuroscience approaches have provided knowledge about biological mechanisms that contribute to OUD-related phenotypes, but the complexity and magnitude of effects in the brain and body remain poorly understood. The gut-brain axis has emerged as a promising target for future therapeutics for several psychiatric conditions, so characterizing the relationship between host genetics and the gut microbiome in the context of OUD will be essential for development of novel treatments. In this review, we describe evidence that interactions between host genetics, the gut microbiome, and immune signaling likely play a key role in mediating opioid-related phenotypes. Studies in humans and model organisms consistently demonstrated that genetic background is a major determinant of gut microbiome composition. Furthermore, the gut microbiome is susceptible to environmental influences such as opioid exposure. Additional work focused on gene by microbiome interactions will be necessary to gain improved understanding of their effects on OUD-related behaviors.
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Affiliation(s)
- Eamonn P Duffy
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA.
| | - Ryan K Bachtell
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA; Department of Psychology and Neuroscience, University of Colorado Boulder, Boulder, CO, USA
| | - Marissa A Ehringer
- Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO, USA; Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
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Marzano V, Mortera SL, Marangelo C, Piazzesi A, Rapisarda F, Pane S, Del Chierico F, Vernocchi P, Romani L, Campana A, Palma P, Putignani L. The metaproteome of the gut microbiota in pediatric patients affected by COVID-19. Front Cell Infect Microbiol 2023; 13:1327889. [PMID: 38188629 PMCID: PMC10766818 DOI: 10.3389/fcimb.2023.1327889] [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: 10/25/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024] Open
Abstract
Introduction The gut microbiota (GM) play a significant role in the infectivity and severity of COVID-19 infection. However, the available literature primarily focuses on adult patients and it is known that the microbiota undergoes changes throughout the lifespan, with significant alterations occurring during infancy and subsequently stabilizing during adulthood. Moreover, children have exhibited milder symptoms of COVID-19 disease, which has been associated with the abundance of certain protective bacteria. Here, we examine the metaproteome of pediatric patients to uncover the biological mechanisms that underlie this protective effect of the GM. Methods We performed nanoliquid chromatography coupled with tandem mass spectrometry on a high resolution analytical platform, resulting in label free quantification of bacterial protein groups (PGs), along with functional annotations via COG and KEGG databases by MetaLab-MAG. Additionally, taxonomic assignment was possible through the use of the lowest common ancestor algorithm provided by Unipept software. Results A COVID-19 GM functional dissimilarity respect to healthy subjects was identified by univariate analysis. The alteration in COVID-19 GM function is primarily based on bacterial pathways that predominantly involve metabolic processes, such as those related to tryptophan, butanoate, fatty acid, and bile acid biosynthesis, as well as antibiotic resistance and virulence. Discussion These findings highlight the mechanisms by which the pediatric GM could contribute to protection against the more severe manifestations of the disease in children. Uncovering these mechanisms can, therefore, have important implications in the discovery of novel adjuvant therapies for severe COVID-19.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonia Piazzesi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Federica Rapisarda
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Stefania Pane
- Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Romani
- Unit of Infectious Disease, Bambino Gesu’ Children’s Hospital, IRCCS, Rome, Italy
| | - Andrea Campana
- Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Paolo Palma
- Research Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
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Marzano V, Levi Mortera S, Vernocchi P, Del Chierico F, Marangelo C, Guarrasi V, Gardini S, Dentici ML, Capolino R, Digilio MC, Di Donato M, Spasari I, Abreu MT, Dallapiccola B, Putignani L. Williams-Beuren syndrome shapes the gut microbiota metaproteome. Sci Rep 2023; 13:18963. [PMID: 37923896 PMCID: PMC10624682 DOI: 10.1038/s41598-023-46052-9] [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: 08/10/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023] Open
Abstract
Williams-Beuren syndrome (WBS) is a rare genetic neurodevelopmental disorder with multi-systemic manifestations. The evidence that most subjects with WBS face gastrointestinal (GI) comorbidities, have prompted us to carry out a metaproteomic investigation of their gut microbiota (GM) profile compared to age-matched healthy subjects (CTRLs). Metaproteomic analysis was carried out on fecal samples collected from 41 individuals with WBS, and compared with samples from 45 CTRLs. Stool were extracted for high yield in bacterial protein group (PG) content, trypsin-digested and analysed by nanoLiquid Chromatography-Mass Spectrometry. Label free quantification, taxonomic assignment by the lowest common ancestor (LCA) algorithm and functional annotations by COG and KEGG databases were performed. Data were statistically interpreted by multivariate and univariate analyses. A WBS GM functional dissimilarity respect to CTRLs, regardless age distribution, was reported. The alterations in function of WBSs GM was primarily based on bacterial pathways linked to carbohydrate transport and metabolism and energy production. Influence of diet, obesity, and GI symptoms was assessed, highlighting changes in GM biochemical patterns, according to WBS subsets' stratification. The LCA-derived ecology unveiled WBS-related functionally active bacterial signatures: Bacteroidetes related to over-expressed PGs, and Firmicutes, specifically the specie Faecalibacterium prausnitzii, linked to under-expressed PGs, suggesting a depletion of beneficial bacteria. These new evidences on WBS gut dysbiosis may offer novel targets for tailored interventions.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Pamela Vernocchi
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Del Chierico
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Chiara Marangelo
- Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Valerio Guarrasi
- GenomeUp s.r.l., Rome, Italy
- Unit of Computer Systems and Bioinformatics, Department of Engineering, University Campus Bio-Medico of Rome, Rome, Italy
| | | | - Maria Lisa Dentici
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Genetics and Rare Diseases Research Division, Medical Genetics Department, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maddalena Di Donato
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Iolanda Spasari
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Maria Teresa Abreu
- Division of Digestive Health and Liver Diseases, Department of Medicine, Crohn's and Colitis Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Bruno Dallapiccola
- Scientific Directorate, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Human Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
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Gómez-Varela D, Xian F, Grundtner S, Sondermann JR, Carta G, Schmidt M. Increasing taxonomic and functional characterization of host-microbiome interactions by DIA-PASEF metaproteomics. Front Microbiol 2023; 14:1258703. [PMID: 37908546 PMCID: PMC10613666 DOI: 10.3389/fmicb.2023.1258703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Metaproteomics is a rapidly advancing field that offers unique insights into the taxonomic composition and the functional activity of microbial communities, and their effects on host physiology. Classically, data-dependent acquisition (DDA) mass spectrometry (MS) has been applied for peptide identification and quantification in metaproteomics. However, DDA-MS exhibits well-known limitations in terms of depth, sensitivity, and reproducibility. Consequently, methodological improvements are required to better characterize the protein landscape of microbiomes and their interactions with the host. Methods We present an optimized proteomic workflow that utilizes the information captured by Parallel Accumulation-Serial Fragmentation (PASEF) MS for comprehensive metaproteomic studies in complex fecal samples of mice. Results and discussion We show that implementing PASEF using a DDA acquisition scheme (DDA-PASEF) increased peptide quantification up to 5 times and reached higher accuracy and reproducibility compared to previously published classical DDA and data-independent acquisition (DIA) methods. Furthermore, we demonstrate that the combination of DIA, PASEF, and neuronal-network-based data analysis, was superior to DDA-PASEF in all mentioned parameters. Importantly, DIA-PASEF expanded the dynamic range towards low-abundant proteins and it doubled the quantification of proteins with unknown or uncharacterized functions. Compared to previous classical DDA metaproteomic studies, DIA-PASEF resulted in the quantification of up to 4 times more taxonomic units using 16 times less injected peptides and 4 times shorter chromatography gradients. Moreover, 131 additional functional pathways distributed across more and even uniquely identified taxa were profiled as revealed by a peptide-centric taxonomic-functional analysis. We tested our workflow on a validated preclinical mouse model of neuropathic pain to assess longitudinal changes in host-gut microbiome interactions associated with pain - an unexplored topic for metaproteomics. We uncovered the significant enrichment of two bacterial classes upon pain, and, in addition, the upregulation of metabolic activities previously linked to chronic pain as well as various hitherto unknown ones. Furthermore, our data revealed pain-associated dynamics of proteome complexes implicated in the crosstalk between the host immune system and the gut microbiome. In conclusion, the DIA-PASEF metaproteomic workflow presented here provides a stepping stone towards a deeper understanding of microbial ecosystems across the breadth of biomedical and biotechnological fields.
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Carneiro L, Marousez L, Van Hul M, Tran LC, De Lamballerie M, Ley D, Cani PD, Knauf C, Lesage J. The Sterilization of Human Milk by Holder Pasteurization or by High Hydrostatic Pressure Processing Leads to Differential Intestinal Effects in Mice. Nutrients 2023; 15:4043. [PMID: 37764826 PMCID: PMC10536938 DOI: 10.3390/nu15184043] [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: 07/13/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Human milk banks (HMBs) provide sterilized donor milk (DM) for the feeding of preterm infants. Most HMBs use the standard method of Holder pasteurization (HoP) performed by heating DM at 62.5 °C for 30 min. High hydrostatic pressure (HHP) processing has been proposed as an alternative to HoP. This study aims to evaluate intestinal barrier integrity and microbiota composition in adult mice subjected to a chronic oral administration of HoP- or HHP-DM. METHODS Mice were treated by daily gavages with HoP- or HHP-DM over seven days. Intestinal barrier integrity was assessed through in vivo 4 kDa FITC-dextran permeability assay and mRNA expression of several tight junctions and mucins in ileum and colon. Cecal short chain fatty acids (SCFAs) and microbiota were analyzed. RESULTS HHP-DM mice displayed decreased intestinal permeability to FITC-dextran and increased ileal mRNA expression levels of two tight junctions (Ocln and Cdh1) and Muc2. In the colon, mRNA expression levels of two tight junctions (Cdh1 and Tjp1) and of two mucins (Muc2 and Muc4) were decreased in HHP-DM mice. Cecal SCFAs and microbiota were not different between groups. CONCLUSIONS HHP processing of DM reinforces intestinal barrier integrity in vivo without affecting gut microbiota and SCFAs production. This study reinforces previous findings showing that DM sterilization through HHP might be beneficial for the intestinal maturation of preterm infants compared with the use of HoP for the treatment of DM.
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Affiliation(s)
- Lionel Carneiro
- INSERM U1220, Institut de Recherche en Santé Digestive (IRSD), Université Paul Sabatier, Toulouse III, CHU Purpan, Place du Docteur Baylac, CS 60039, CEDEX 3, 31024 Toulouse, France; (L.C.); (C.K.)
- NeuroMicrobiota, International Research Program (IRP) INSERM/UCLouvain, 31024 Toulouse, France; (M.V.H.); (P.D.C.)
| | - Lucie Marousez
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, 59000 Lille, France; (L.M.); (D.L.)
| | - Matthias Van Hul
- NeuroMicrobiota, International Research Program (IRP) INSERM/UCLouvain, 31024 Toulouse, France; (M.V.H.); (P.D.C.)
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), UCLouvain (Université catholique de Louvain), 1200 Brussels, Belgium
- WELBIO Department, WEL Research Institute (WELRI), Avenue Pasteur, 6, 1300 Wavre, Belgium
| | - Léa Chantal Tran
- Division of Gastroenterology Hepatology and Nutrition, Department of Paediatrics, Jeanne de Flandre Children’s Hospital, CHU Lille, 59000 Lille, France;
| | | | - Delphine Ley
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, 59000 Lille, France; (L.M.); (D.L.)
- Division of Gastroenterology Hepatology and Nutrition, Department of Paediatrics, Jeanne de Flandre Children’s Hospital, CHU Lille, 59000 Lille, France;
| | - Patrice D. Cani
- NeuroMicrobiota, International Research Program (IRP) INSERM/UCLouvain, 31024 Toulouse, France; (M.V.H.); (P.D.C.)
- Metabolism and Nutrition Research Group, Louvain Drug Research Institute (LDRI), UCLouvain (Université catholique de Louvain), 1200 Brussels, Belgium
- WELBIO Department, WEL Research Institute (WELRI), Avenue Pasteur, 6, 1300 Wavre, Belgium
- Institute of Experimental and Clinical Research (IREC), UCLouvain (Université catholique de Louvain), 1200 Brussels, Belgium
| | - Claude Knauf
- INSERM U1220, Institut de Recherche en Santé Digestive (IRSD), Université Paul Sabatier, Toulouse III, CHU Purpan, Place du Docteur Baylac, CS 60039, CEDEX 3, 31024 Toulouse, France; (L.C.); (C.K.)
- NeuroMicrobiota, International Research Program (IRP) INSERM/UCLouvain, 31024 Toulouse, France; (M.V.H.); (P.D.C.)
| | - Jean Lesage
- Univ. Lille, Inserm, CHU Lille, U1286-INFINITE-Institute for Translational Research in Inflammation, 59000 Lille, France; (L.M.); (D.L.)
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Arnesen H, Markussen T, Birchenough G, Birkeland S, Nyström EEL, Hansson GC, Carlsen H, Boysen P. Microbial experience through housing in a farmyard-type environment alters intestinal barrier properties in mouse colons. Sci Rep 2023; 13:13701. [PMID: 37607995 PMCID: PMC10444815 DOI: 10.1038/s41598-023-40640-5] [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: 05/16/2023] [Accepted: 08/14/2023] [Indexed: 08/24/2023] Open
Abstract
To close the gap between ultra-hygienic research mouse models and the much more environmentally exposed conditions of humans, we have established a system where laboratory mice are raised under a full set of environmental factors present in a naturalistic, farmyard-type habitat-a process we have called feralization. In previous studies we have shown that feralized (Fer) mice were protected against colorectal cancer when compared to conventionally reared laboratory mice (Lab). However, the protective mechanisms remain to be elucidated. Disruption of the protective intestinal barrier is an acknowledged player in colorectal carcinogenesis, and in the current study we assessed colonic mucosal barrier properties in healthy, feralized C57BL/6JRj male mice. While we found no effect of feralization on mucus layer properties, higher expression of genes encoding the mucus components Fcgbp and Clca1 still suggested mucus enforcement due to feralization. Genes encoding other proteins known to be involved in bacterial defense (Itln1, Ang1, Retnlb) and inflammatory mechanisms (Zbp1, Gsdmc2) were also higher expressed in feralized mice, further suggesting that the Fer mice have an altered intestinal mucosal barrier. These findings demonstrate that microbial experience conferred by housing in a farmyard-type environment alters the intestinal barrier properties in mice possibly leading to a more robust protection against disease. Future studies to unravel regulatory roles of feralization on intestinal barrier should aim to conduct proteomic analyses and in vivo performance of the feralized mice intestinal barrier.
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Affiliation(s)
- Henriette Arnesen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Turhan Markussen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - George Birchenough
- Mucin Biology Group, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Signe Birkeland
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Elisabeth E L Nyström
- Mucin Biology Group, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Gunnar C Hansson
- Mucin Biology Group, Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Harald Carlsen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences (NMBU), Ås, Norway
| | - Preben Boysen
- Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Ås, Norway.
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10
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Verschaffelt P, Tanca A, Abbondio M, Van Den Bossche T, Moortele TV, Dawyndt P, Martens L, Mesuere B. Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses. J Proteome Res 2023; 22:2620-2628. [PMID: 37459443 DOI: 10.1021/acs.jproteome.3c00091] [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] [Indexed: 08/05/2023]
Abstract
Unipept Desktop 2.0 is the most recent iteration of the Unipept Desktop tool that adds support for the analysis of metaproteogenomics datasets. Unipept Desktop now supports the automatic construction of targeted protein reference databases that only contain proteins (originating from the UniProtKB resource) associated with a predetermined list of taxa. This improves both the taxonomic and functional resolution of a metaproteomic analysis and yields several technical advantages. By limiting the proteins present in a reference database, it is also possible to perform (meta)proteogenomics analyses. Since the protein reference database resides on the user's local machine, they have complete control over the database used during an analysis. Data no longer need to be transmitted over the Internet, decreasing the time required for an analysis and better safeguarding privacy-sensitive data. As a proof of concept, we present a case study in which a human gut metaproteome dataset is analyzed with Unipept Desktop 2.0 using different targeted databases based on matched 16S rRNA gene sequencing data.
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Affiliation(s)
- Pieter Verschaffelt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
- VIB - UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
| | - Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy
| | | | - Tibo Vande Moortele
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Peter Dawyndt
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB - UGent Center for Medical Biotechnology, VIB, 9052 Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium
| | - Bart Mesuere
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
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11
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Han J, Wu Q, Wang Z, Lu C, Zhou J, Li Y, Ming T, Zhang Z, Su X. Spatial distribution of gut microbiota in mice during the occurrence and remission of hyperuricemia. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023; 103:4077-4084. [PMID: 36502373 DOI: 10.1002/jsfa.12383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 10/08/2022] [Accepted: 12/11/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND Previous studies have shown that anserine can alleviate hyperuricemia by changing the fecal microbiota of hyperuricemic mice. TOPIC However, the fecal microbiota could not fully represent the distribution of the whole gut microbiota. Knowing the spatial distribution of the gastrointestinal tract microbiota is therefore important for understanding its action in the occurrence and remission of hyperuricemia. METHODS This study provides a comprehensive map of the most common bacterial communities that colonize different parts of the mouse gastrointestinal tract (stomach, duodenum, ileum, cecum, and colon) using a modern methodological approach. RESULTS The stomach, colon, and cecum showed the greatest richness and diversity in bacterial species. Three clusters of bacterial populations were observed along the digestive system: (1) in the stomach, (2) in the duodenum and ileum, and (3) in the colon and cecum. A high purine solution changed the composition and abundance of the digestive tract microbiota, and anserine relieved hyperuricemia by restoring the homeostasis of the digestive tract microbiota, especially improving the abundance of probiotics in the digestive tract. IMPLICATION This could be the starting point for further research on the regulation of hyperuricemia by gut microbiota with the ultimate goal of promoting health and welfare. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Jiaojiao Han
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Qiaoli Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Ziyan Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Chenyang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Jun Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Ye Li
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Tinghong Ming
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Zhen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
| | - Xiurong Su
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, China
- School of Marine Science, Ningbo University, Ningbo, China
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12
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Sonke A, Trembath-Reichert E. Expanding the taxonomic and environmental extent of an underexplored carbon metabolism-oxalotrophy. Front Microbiol 2023; 14:1161937. [PMID: 37213515 PMCID: PMC10192776 DOI: 10.3389/fmicb.2023.1161937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
Oxalate serves various functions in the biological processes of plants, fungi, bacteria, and animals. It occurs naturally in the minerals weddellite and whewellite (calcium oxalates) or as oxalic acid. The environmental accumulation of oxalate is disproportionately low compared to the prevalence of highly productive oxalogens, namely plants. It is hypothesized that oxalotrophic microbes limit oxalate accumulation by degrading oxalate minerals to carbonates via an under-explored biogeochemical cycle known as the oxalate-carbonate pathway (OCP). Neither the diversity nor the ecology of oxalotrophic bacteria is fully understood. This research investigated the phylogenetic relationships of the bacterial genes oxc, frc, oxdC, and oxlT, which encode key enzymes for oxalotrophy, using bioinformatic approaches and publicly available omics datasets. Phylogenetic trees of oxc and oxdC genes demonstrated grouping by both source environment and taxonomy. All four trees included genes from metagenome-assembled genomes (MAGs) that contained novel lineages and environments for oxalotrophs. In particular, sequences of each gene were recovered from marine environments. These results were supported with marine transcriptome sequences and description of key amino acid residue conservation. Additionally, we investigated the theoretical energy yield from oxalotrophy across marine-relevant pressure and temperature conditions and found similar standard state Gibbs free energy to "low energy" marine sediment metabolisms, such as anaerobic oxidation of methane coupled to sulfate reduction. These findings suggest further need to understand the role of bacterial oxalotrophy in the OCP, particularly in marine environments, and its contribution to global carbon cycling.
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13
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Functional and Taxonomic Traits of the Gut Microbiota in Type 1 Diabetes Children at the Onset: A Metaproteomic Study. Int J Mol Sci 2022; 23:ijms232415982. [PMID: 36555624 PMCID: PMC9787575 DOI: 10.3390/ijms232415982] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/02/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Type 1 diabetes (T1D) is a chronic autoimmune metabolic disorder with onset in pediatric/adolescent age, characterized by insufficient insulin production, due to a progressive destruction of pancreatic β-cells. Evidence on the correlation between the human gut microbiota (GM) composition and T1D insurgence has been recently reported. In particular, 16S rRNA-based metagenomics has been intensively employed in the last decade in a number of investigations focused on GM representation in relation to a pre-disease state or to a response to clinical treatments. On the other hand, few works have been published using alternative functional omics, which is more suitable to provide a different interpretation of such a relationship. In this work, we pursued a comprehensive metaproteomic investigation on T1D children compared with a group of siblings (SIBL) and a reference control group (CTRL) composed of aged matched healthy subjects, with the aim of finding features in the T1D patients' GM to be related with the onset of the disease. Modulated metaproteins were found either by comparing T1D with CTRL and SIBL or by stratifying T1D by insulin need (IN), as a proxy of β-cells damage, showing some functional and taxonomic traits of the GM, possibly related to the disease onset at different stages of severity.
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14
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Besaury L, Bocquart M, Rémond C. Isolation of Saccharibacillus WB17 strain from wheat bran phyllosphere and genomic insight into the cellulolytic and hemicellulolytic complex of the Saccharibacillus genus. Braz J Microbiol 2022; 53:1829-1842. [PMID: 36040685 PMCID: PMC9679120 DOI: 10.1007/s42770-022-00819-w] [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: 02/03/2022] [Accepted: 08/23/2022] [Indexed: 01/13/2023] Open
Abstract
The microorganisms living on the phyllosphere (the aerial part of the plants) are in contact with the lignocellulosic plant cell wall and might have a lignocellulolytic potential. We isolated a Saccharibacillus strain (Saccharibacillus WB17) from wheat bran phyllosphere and its cellulolytic and hemicellulolytic potential was investigated during growth onto wheat bran. Five other type strains from that genus selected from databases were also cultivated onto wheat bran and glucose. Studying the chemical composition of wheat bran residues by FTIR after growth of the six strains showed an important attack of the stretching C-O vibrations assigned to polysaccharides for all the strains, whereas the C = O bond/esterified carboxyl groups were not impacted. The genomic content of the strains showed that they harbored several CAZymes (comprised between 196 and 276) and possessed four of the fifth modules reflecting the presence of a high diversity of enzymes families. Xylanase and amylase activities were the most active enzymes with values reaching more than 4746 ± 1400 mIU/mg protein for the xylanase activity in case of Saccharibacillus deserti KCTC 33693 T and 452 ± 110 mIU/mg protein for the amylase activity of Saccharibacillus WB17. The total enzymatic activities obtained was not correlated to the total abundance of CAZyme along that genus. The Saccharibacillus strains harbor also some promising proteins in the GH30 and GH109 modules with potential arabinofuranosidase and oxidoreductase activities. Overall, the genus Saccharibacillus and more specifically the Saccharibacillus WB17 strain represent biological tools of interest for further biotechnological applications.
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Affiliation(s)
- Ludovic Besaury
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France.
| | - Mathilde Bocquart
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
| | - Caroline Rémond
- Université de Reims Champagne Ardenne, INRAE, FARE, UMR A 614, Chaire AFERE, 51097, Reims, France
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15
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Gu J, Cui S, Tang X, Liu Z, Zhao J, Zhang H, Mao B, Chen W. Fructooligosaccharides (FOS) significantly increased the relative abundance of intestinal B. pseudolongum in mice with different genotypes. Curr Res Food Sci 2022; 5:2178-2189. [PMID: 36387600 PMCID: PMC9661384 DOI: 10.1016/j.crfs.2022.10.030] [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: 06/27/2022] [Revised: 09/22/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Fructooligosaccharides (FOS) promote the proliferation of Bifidobacterium, especially Bifidobacterium pseudolongum in C57BL/6J mice. However, the response of intestinal microbes to FOS is influenced by host genotypes. Therefore, we compared the intestinal microbiota of four commonly used mice before and after FOS intervention, including C57BL/6J, BALB/c, Institute Cancer Research (ICR), and Kunming (KM) mice. The intestinal microbiota of the four genotypes exhibited similarities in composition but differences in relative abundance. Bifidobacterium was significantly increased to different degrees in the four genotypes of mice after FOS intervention, and Akkermansia and Bacteroides were also significantly increased in BALB/c and KM mice. Lactobacillus and Alistipes levels were unchanged or decreased. Within the genus Bifidobacterium, B. pseudolongum was the dominant species in the four genotypes of mice and proliferated significantly after FOS intervention, with dramatic proliferation in C57BL/6J mice (9.49%). Furthermore, eight strains of B. pseudolongum were screened from the feces of mice with four genotypes, and there was a great difference in the ability and manner of utilizing FOS among the strains. The strains from C57BL/6J mice exhibited the strongest utilization of 1-kestose (GF2), whereas other strains could utilize both GF2 and nistose (GF3) weakly. The gut microbial analysis of mice with different genotypes complemented our previous studies. The results provided the background strains of the different mouse genotypes and suggested a correlation between the utilization ability and the response of the strains to FOS. Further studies on the utilization ability of strains and competition in the intestine will contribute to the understanding of the mechanisms of the intestinal microbial response to diet. The intestinal microbiota is similar in composition for mice of different genotypes. B. pseudolongum predominates in bifidobacteria in mice of different genotypes. The relative abundance of B. pseudolongum increases after FOS intake. B. pseudolongum strains show different abilities in utilizing FOS.
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16
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Co-administration of Lactobacillus gasseri KBL697 and tumor necrosis factor-alpha inhibitor infliximab improves colitis in mice. Sci Rep 2022; 12:9640. [PMID: 35688918 PMCID: PMC9187735 DOI: 10.1038/s41598-022-13753-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/13/2022] [Indexed: 11/08/2022] Open
Abstract
Inflammatory bowel disease (IBD) refers to disorders involving chronic inflammation of the gastrointestinal tract. Well-established treatments for IBD have not yet to be suggested. To address this gap, we investigated the effects of co-administration of Lactobacillus gasseri (L. gasseri) KBL697 and infliximab (IFX), the first approved tumor necrosis factor (TNF)-alpha inhibitor, on the dextran sodium sulfate-induced colitis mouse model. 2 × 109 colony-forming units/g of L. gasseri KBL697 were administered to seven-week-old female C57BL/6J mice daily by oral gavage. On day three, IFX (5 mg/kg) suspended in 1 × PBS (200 µL) was intravenously injected in the IFX-treated group and all mice were sacrificed on day nine. Co-administration of L. gasseri KBL697 and IFX improved colitis symptoms in mice, including body weight, disease activity index, colon length, and histology score. Additionally, pro-inflammatory cytokines, such as interferon-gamma, interleukin (IL)-2, IL-6, IL-17A, and TNF were significantly decreased, while IL-10, an anti-inflammatory cytokine, was increased. Expression levels of tight junction genes and CD4 + CD25 + Foxp3 + T regulatory cells in the mesenteric lymph nodes were synergistically upregulated with the combined treatment. Furthermore, co-administered mice displayed altered cecum microbial diversity and composition with increases in the genus Prevotella. Related changes in the predicted amino and nucleic acid metabolic pathways were also evident, along with increased acetate and butyrate level. Therefore, the synergistic effect of L. gasseri KBL697 and IFX co-administration is a possible method of prevention and treatment for IBD.
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17
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Liu Y, Tian X, Daniel RC, Okeugo B, Armbrister SA, Luo M, Taylor CM, Wu G, Rhoads JM. Impact of probiotic Limosilactobacillus reuteri DSM 17938 on amino acid metabolism in the healthy newborn mouse. Amino Acids 2022; 54:1383-1401. [PMID: 35536363 DOI: 10.1007/s00726-022-03165-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/19/2022] [Indexed: 12/15/2022]
Abstract
We studied the effect of feeding a single probiotic Limosilactobacillus reuteri DSM 17938 (LR 17938) on the luminal and plasma levels of amino acids and their derivatives in the suckling newborn mouse, using gas chromatography and high-performance liquid chromatography. We found that LR 17938 increased the relative abundance of many amino acids and their derivatives in stool, while it simultaneously significantly reduced the plasma levels of three amino acids (serine, citrulline, and taurine). Many peptides and dipeptides were increased in stool and plasma, notably gamma-glutamyl derivatives of amino acids, following ingestion of the LR 17938. Gamma-glutamyl transformation of amino acids facilitates their absorption. LR 17938 significantly upregulated N-acetylated amino acids, the levels of which could be useful biomarkers in plasma and warrant further investigation. Specific fecal microbiota were associated with higher levels of fecal amino acids and their derivatives. Changes in luminal and circulating levels of amino acid derivatives, polyamines, and tryptophan metabolites may be mechanistically related to probiotic efficacy.
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Affiliation(s)
- Yuying Liu
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 3.140A, Houston, TX, 77030, USA.
| | - Xiangjun Tian
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rhea C Daniel
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 3.140A, Houston, TX, 77030, USA
| | - Beanna Okeugo
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 3.140A, Houston, TX, 77030, USA
| | - Shabba A Armbrister
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 3.140A, Houston, TX, 77030, USA
| | - Meng Luo
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Christopher M Taylor
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, LA, USA
| | - Guoyao Wu
- Department of Animal Science, Texas A&M University, College Station, TX, USA
| | - J Marc Rhoads
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin Street, MSB 3.140A, Houston, TX, 77030, USA
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Ma S, Shu X, Wang WX. Multi-omics reveals the regulatory mechanisms of zinc exposure on the intestine-liver axis of golden pompano Trachinotus ovatus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 816:151497. [PMID: 34752869 DOI: 10.1016/j.scitotenv.2021.151497] [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: 09/27/2021] [Revised: 11/01/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Metal zinc (Zn) has been the focus of many environmental toxicological studies, but there are limited studies on its potential dietary molecular toxicity and physiology. The present study was the first to use multi-omics-based approaches to explore the fish intestine-liver axis under dietary Zn exposure. Golden pompano Trachinotus ovatus were exposed to different dietary concentrations (78.4, 134.6, and 161.4 mg/kg as the control, low-dose Zn, and high-dose Zn groups, respectively) of Zn for 4-week. Low-dose Zn exposure significantly promoted the fish growth, whereas the high-dose Zn exposure reduced the fish growth. Co-analysis of 16S diversity, metagenome and transcriptome showed that the low-dose Zn enriched the intestinal microflora and changed the dominant microflora abundances (Proteobacteria, Fusobacteria, Firmicutes and Bacteroidetes), as well as activated the growth hormone metabolism in the liver. Meanwhile, the high-dose of Zn caused the intestinal microbiota dysbiosis, activated the Type VI secretion systems (T6SSs), and further triggered the oxidative stress response, immunity, and antiviral function of the liver. Multi-omics revealed the interference of long-term Zn dietary exposure on the intestine-liver axis. There was an apparent homeostasis of Zn accumulation in the fish tissues, but the window of dietary Zn nutritional requirements versus toxicity appeared to be narrow for the golden pompano. These results provided new insight into the adverse effects and regulatory mechanisms of dietary Zn requirements and toxicity in marine fish.
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Affiliation(s)
- Shuoli Ma
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Xugang Shu
- School of Chemistry and Chemical Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Wen-Xiong Wang
- School of Energy and Environment and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China; Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.
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Li L, lv X, Han X, Sun C, An K, Gao W, Xia Z. Effect of Dietary Bacillus licheniformis Supplementation on Growth Performance and Microbiota Diversity of Pekin Ducks. Front Vet Sci 2022; 9:832141. [PMID: 35265695 PMCID: PMC8899091 DOI: 10.3389/fvets.2022.832141] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
This experiment was conducted to investigate the effects of different concentrations of Bacillus licheniformis (B. licheniformis) on growth performance and microbiota diversity of Pekin ducks. Three hundred 1-day-old healthy Pekin ducks were randomly divided into 5 groups with 6 replicates per group and 10 ducks per replicate. The five treatments supplemented with basal diets containing: either 0 (group CON), 200 (group LLB), 400 (group MLB), and 800 (group HLB) mg/kg B. licheniformis or 150 mg/kg aureomycin (group ANT) for 42 days, respectively, and were sacrificed and sampled in the morning of the 42nd day for detection of relevant indexes. The results showed as follows: The feed conversion ratio of the LLB group and MLB groups were lower than the CON group (P < 0.05). The body weight and average daily feed intake of the MLB group were significantly higher than that of the CON group and ANT group (P < 0.05). Compared with the CON group, the MLB group significantly increased the content of IgA (P < 0.05) and proinflammatory IL-6 were significantly decreased (P < 0.05), besides, the activity of SOD and T-AOC were also significantly increased in the MLB group (P < 0.05). The 16S rRNA analysis showed that B. licheniformis treatments had no effect (P > 0.05) on the alpha diversities of the intestine. The addition of B. licheniformis had a dynamic effect on the abundance of cecal microflora of Pekin ducks, and 1-21 d increased the diversity of microflora, while 21d-42 d decreased it. Compared with the CON group, the relative abundance of Epsilonbacteraeota in the MLB group was significantly increased on Day 21 (P < 0.05), and that of Tenericutes in the LLB group was significantly increased as well (P < 0.05). At 42 d, the relative abundance of Bacteroidetes in LLB, MBL, HBL, and ANT groups was significantly increased (P < 0.05). In addition, the addition of B. licheniformis increased the amount of SCAF-producing bacteria in the intestinal microbiota, such as Lachnospiraceae, Collinsella, Christensenellaceae, and Bilophila. The PICRUSt method was used to predict the intestinal microbiota function, and it was found that lipid transport and metabolism of intestinal microbiota in the MLB group were significantly affected. Overall, these results suggest diet supplemented with B. licheniformis improved growth performance, immune status, antioxidant capacity, and modulated intestinal microbiota in Pekin ducks. The optimal dietary supplement dose is 400 mg/kg.
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Affiliation(s)
- Lei Li
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xueze lv
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- Beijing General Station of Animal Husbandry, Beijing, China
| | - Xu Han
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Chenglei Sun
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Keying An
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenwen Gao
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhaofei Xia
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- *Correspondence: Zhaofei Xia
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Nalpas N, Hoyles L, Anselm V, Ganief T, Martinez-Gili L, Grau C, Droste-Borel I, Davidovic L, Altafaj X, Dumas ME, Macek B. An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. Gut Microbes 2022; 13:1994836. [PMID: 34763597 PMCID: PMC8726736 DOI: 10.1080/19490976.2021.1994836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Intestinal microbiota plays a key role in shaping host homeostasis by regulating metabolism, immune responses and behavior. Its dysregulation has been associated with metabolic, immune and neuropsychiatric disorders and is accompanied by changes in bacterial metabolic regulation. Although proteomics is well suited for analysis of individual microbes, metaproteomics of fecal samples is challenging due to the physical structure of the sample, presence of contaminating host proteins and coexistence of hundreds of taxa. Furthermore, there is a lack of consensus regarding preparation of fecal samples, as well as downstream bioinformatic analyses following metaproteomics data acquisition. Here we assess sample preparation and data analysis strategies applied to mouse feces in a typical mass spectrometry-based metaproteomic experiment. We show that subtle changes in sample preparation protocols may influence interpretation of biological findings. Two-step database search strategies led to significant underestimation of false positive protein identifications. Unipept software provided the highest sensitivity and specificity in taxonomic annotation of the identified peptides of unknown origin. Comparison of matching metaproteome and metagenome data revealed a positive correlation between protein and gene abundances. Notably, nearly all functional categories of detected protein groups were differentially abundant in the metaproteome compared to what would be expected from the metagenome, highlighting the need to perform metaproteomics when studying complex microbiome samples.
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Affiliation(s)
- Nicolas Nalpas
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Lesley Hoyles
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Department of Biosciences, Nottingham Trent University, Nottingham, UK
| | - Viktoria Anselm
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Tariq Ganief
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany
| | - Laura Martinez-Gili
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Cristina Grau
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain
| | | | | | - Xavier Altafaj
- Pharmacology unit, Bellvitge Biomedical Research Institute, University of Barcelona, Barcelona, Spain,Neurophysiology Unit, University of Barcelona – Idibaps, Barcelona, Spain
| | - Marc-Emmanuel Dumas
- Biomolecular Medicine Section, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK,Genomic and Environmental Medicine, National Heart & Lung Institute, Faculty of Medicine, Imperial College London, London, UK,European Genomic Institute for Diabetes, Inserm Umr 1283, Cnrs Umr 8199, Institut Pasteur De Lille, Lille University Hospital, University of Lille, Lille, France
| | - Boris Macek
- Proteome Center Tuebingen, University of Tuebingen, Tuebingen, Germany,CONTACT Boris Macek Proteome Center Tuebingen, Interfaculty Institute for Cell Biology, Auf Der Morgenstelle 15, Tuebingen72076, Germany
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21
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Tanca A, Abbondio M, Fiorito G, Pira G, Sau R, Manca A, Muroni MR, Porcu A, Scanu AM, Cossu-Rocca P, De Miglio MR, Uzzau S. Metaproteomic Profile of the Colonic Luminal Microbiota From Patients With Colon Cancer. Front Microbiol 2022; 13:869523. [PMID: 35495697 PMCID: PMC9048685 DOI: 10.3389/fmicb.2022.869523] [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: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies have provided evidence of interactions among the gut microbiota (GM), local host immune cells, and intestinal tissues in colon carcinogenesis. However, little is known regarding the functions exerted by the GM in colon cancer (CC), particularly with respect to tumor clinical classification and lymphocyte infiltration. In addition, stool, usually employed as a proxy of the GM, cannot fully represent the original complexity of CC microenvironment. Here, we present a pilot study aimed at characterizing the metaproteome of CC-associated colonic luminal contents and identifying its possible associations with CC clinicopathological features. Colonic luminal contents were collected from 24 CC tissue specimens immediately after surgery. Samples were analyzed by shotgun metaproteomics. Almost 30,000 microbial peptides were quantified in the samples, enabling the achievement of the taxonomic and functional profile of the tumor-associated colonic luminal metaproteome. Upon sample aggregation based on tumor stage, grade, or tumor-infiltrating lymphocytes (TILs), peptide sets enabling discrimination of sample groups were identified through discriminant analysis (DA). As a result, Bifidobacterium and Bacteroides fragilis were significantly enriched in high-stage and high-grade CC, respectively. Among metabolic functions, formate-tetrahydrofolate ligase was significantly associated with high-stage CC. Finally, based on the results of this pilot study, we assessed the optimal sample size for differential metaproteomic studies analyzing colonic luminal contents. In conclusion, we provide a detailed picture of the microbial and host components of the colonic luminal proteome and propose promising associations between GM taxonomic/functional features and CC clinicopathological features. Future studies will be needed to verify the prognostic value of these data and to fully exploit the potential of metaproteomics in enhancing our knowledge concerning CC progression.
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Affiliation(s)
- Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanni Fiorito
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Medical Research Council (MRC), Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Giovanna Pira
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Rosangela Sau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Alessandra Manca
- Department of Pathology, Azienda Ospedaliero-Universitaria di Sassari, Sassari, Italy
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy.,Surgical Pathology Unit, Department of Diagnostic Services, "Giovanni Paolo II" Hospital, Area Socio-Sanitaria Locale (ASSL) Olbia-Azienda per la Tutela della Salute (ATS) Sardegna, Olbia, Italy
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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22
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Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota. NPJ Biofilms Microbiomes 2021; 7:85. [PMID: 34862421 PMCID: PMC8642412 DOI: 10.1038/s41522-021-00256-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 11/03/2021] [Indexed: 12/17/2022] Open
Abstract
Diet is a key factor influencing gut microbiota (GM) composition and functions, which in turn affect host health. Among dietary regimens, time-restricted (TR) feeding has been associated to numerous health benefits. The impact of TR feeding on the GM composition has been mostly explored by means of metagenomic sequencing. To date, however, little is known about the modulation of GM functions by this dietary regimen. Here, we analyzed the effects of TR feeding on GM functions by evaluating protein expression changes in a rat model through a metaproteomic approach. We observed that TR feeding has a relevant impact on GM functions, specifically leading to an increased abundance of several enzymes involved in carbohydrate and protein metabolism and expressed by Lactobacillus spp. and Akkermansia muciniphila. Taken together, these results contribute to deepening our knowledge about the key relationship between diet, GM, and health.
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Sciurba JD, Chlipala GE, Green SJ, Delaney MA, Fortman JD, Purcell JE. Evaluation of Effects of Laboratory Disinfectants on Mouse Gut Microbiota. Comp Med 2021; 71:492-501. [PMID: 34763749 DOI: 10.30802/aalas-cm-21-000051] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Disturbances in the gut microbiota are known to be associated with numerous human diseases. Mice have proven to be an invaluable tool for investigating the role of the gut microbiota in disease processes. Nonexperimental factors related to maintaining mice in the laboratory environment are increasingly being shown to have inadvertent effects on the gut microbiotaand may function as confounding variables. Microisolation technique is a term used to describe the common biosecuritypractice of spraying gloved hands with disinfectant before handling research mice. This practice prevents contamination with pathogenic microorganisms. To investigate if exposure to disinfectants can affect the mouse gut microbiota, C57BL/6 micewere exposed daily for 27 consecutive days to commonly used laboratory disinfectants through microisolation technique.The effects of 70% ethanol and disinfectant products containing chlorine dioxide, hydrogen peroxide, or potassium peroxymonosulfate were each evaluated. Fecal pellets were collected after 7, 14, 21, and 28 d of disinfectant exposure, and cecal contents were collected at day 28. DNA extractions were performed on all cecal and fecal samples, and microbial community structure was characterized using 16S ribosomal RNA amplicon sequencing. Alpha and β diversity metrics and taxon-level analyses were used to evaluate differences in microbial communities. Disinfectant had a small but significant effect on fecal microbial communities compared with sham-exposed controls, and effects varied by disinfectant type. In general, longerexposure times resulted in greater changes in the fecal microbiota. Effects on the cecal microbiota were less pronounced and only seen with the hydrogen peroxide and potassium peroxymonosulfate disinfectants. These results indicate that laboratory disinfectant use should be considered as a potential factor that can affect the mouse gut microbiota.
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24
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Bowerman KL, Knowles SCL, Bradley JE, Baltrūnaitė L, Lynch MDJ, Jones KM, Hugenholtz P. Effects of laboratory domestication on the rodent gut microbiome. ISME COMMUNICATIONS 2021; 1:49. [PMID: 36747007 PMCID: PMC9723573 DOI: 10.1038/s43705-021-00053-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/22/2021] [Accepted: 09/03/2021] [Indexed: 05/01/2023]
Abstract
The domestication of the laboratory mouse has influenced the composition of its native gut microbiome, which is now known to differ from that of its wild ancestor. However, limited exploration of the rodent gut microbiome beyond the model species Mus musculus has made it difficult to interpret microbiome variation in a broader phylogenetic context. Here, we analyse 120 de novo and 469 public metagenomically-sequenced faecal and caecal samples from 16 rodent hosts representing wild, laboratory and captive lifestyles. Distinct gut bacterial communities were observed between rodent host genera, with broadly distributed species originating from the as-yet-uncultured bacterial genera UBA9475 and UBA2821 in the families Oscillospiraceae and Lachnospiraceae, respectively. In laboratory mice, Helicobacteraceae were generally depleted relative to wild mice and specific Muribaculaceae populations were enriched in different laboratory facilities, suggesting facility-specific outgrowths of this historically dominant rodent gut family. Several bacterial families of clinical interest, including Akkermansiaceae, Streptococcaceae and Enterobacteriaceae, were inferred to have gained over half of their representative species in mice within the laboratory environment, being undetected in most wild rodents and suggesting an association between laboratory domestication and pathobiont emergence.
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Affiliation(s)
- Kate L Bowerman
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
| | | | | | | | | | - Kathryn M Jones
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Philip Hugenholtz
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, Australia.
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25
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Wang S, Liu Y, Li J, Zhao L, Yan W, Lin B, Guo X, Wei Y. Fusobacterium nucleatum Acts as a Pro-carcinogenic Bacterium in Colorectal Cancer: From Association to Causality. Front Cell Dev Biol 2021; 9:710165. [PMID: 34490259 PMCID: PMC8417943 DOI: 10.3389/fcell.2021.710165] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is a common cancer worldwide with complex etiology. Fusobacterium nucleatum (F. nucleatum), an oral symbiotic bacterium, has been linked with CRC in the past decade. A series of gut microbiota studies show that CRC patients carry a high abundance of F. nucleatum in the tumor tissue and fecal, and etiological studies have clarified the role of F. nucleatum as a pro-carcinogenic bacterium in various stages of CRC. In this review, we summarize the biological characteristics of F. nucleatum and the epidemiological associations between F. nucleatum and CRC, and then highlight the mechanisms by which F. nucleatum participates in CRC progression, metastasis, and chemoresistance by affecting cancer cells or regulating the tumor microenvironment (TME). We also discuss the research gap in this field and give our perspective for future studies. These findings will pave the way for manipulating gut F. nucleatum to deal with CRC in the future.
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Affiliation(s)
- Shuang Wang
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang Liu
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jun Li
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lei Zhao
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Yan
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Baiqiang Lin
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiao Guo
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunwei Wei
- Department of Oncological and Endoscopic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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26
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Liu Y, Liu C, An K, Gong X, Xia Z. Effect of Dietary Clostridium butyricum Supplementation on Growth Performance, Intestinal Barrier Function, Immune Function, and Microbiota Diversity of Pekin Ducks. Animals (Basel) 2021; 11:ani11092514. [PMID: 34573480 PMCID: PMC8471152 DOI: 10.3390/ani11092514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/19/2021] [Accepted: 08/21/2021] [Indexed: 12/28/2022] Open
Abstract
Simple Summary In poultry farming, the use of prophylactic antibiotics can lead to increased resistance, so probiotics are a good alternative. Clostridium butyricum (C. butyricum) has been widely used to improve the gut health of animals. Therefore, we carried out the current study of Pekin ducks supplemented with C. butyricum for a period of 42 days. Here, we found a clear increase in the growth performance of Pekin ducks supplemented with C. butyricum. Moreover, a high level of secretory IgA, IgM, IgG, IL-4, and IL-10 and comparatively higher short-chain fatty acids (SCFAs) and intestinal tight junction changes were found in Pekin ducks supplemented with C. butyricum. The gut microbial diversity of Pekin ducks supplemented with C. butyricum was clearly different than that of Pekin ducks fed a non-C. butyricum diet. In conclusion, our findings suggest that 400 mg/kg C. butyricum supplementation improved the intestinal health of Pekin ducks by increasing the α-diversity of intestinal microbiota, enhancing the SCFAs contents, and strengthening the intestinal barrier function and immune systems indicating that 400 mg/kg C. butyricum might be a preferable antibiotic alternative for commercial application. Abstract Clostridium butyricum (C. butyricum) is increasingly being used to test the promotion of the gut health of animals. However, the modes of action for such applications for waterfowl remain unclear. Thus, we investigated whether or not intestinal barrier function, immune-related gene expression, and the diversity of the intestinal microbiota in Pekin ducks varied under C. butyricum supplementation. A total of 500 ducks were randomly assigned into five treatments supplemented with basal diets containing: either 0 (group Control), 200 (group CB200), 400 (group CB400) and 600 (group CB600) mg/kg C. butyricum or 150 mg/kg aureomycin (group A150) for 42 days. In comparison with the control group, C. butyricum supplementation enhanced the growth performance and intestinal villus height of Pekin ducks at 42 d. Serum immune indexes and fecal short-chain fatty acids (SCFAs) were all improved at both 21 d and 42 d after C. butyricum addition. The mRNA expression levels of Mucin2, Zonula occludens-1 (ZO-1), Caudin-3, and Occludin increased at 21 d and 42 d and the mRNA expression levels of IL-4 and IL-10 only increased at 42 d after C. butyricum addition. Dietary C. butyricum also resulted in an increase in the number of diversities of operational taxonomic units (OTUs), and an increase in the α-diversity of intestinal microbiota. The addition of C. butyricum altered the composition of the intestinal microbiota from 21 d to 42 d. The relative abundance of Firmicutes and Bacteroidetes showed little changes among groups; however, the relative abundance of Firmicutes/Bacteroidetes were found to have been significantly different between the 21 d and 42 d. C. butyricum administration improved the intestinal health of Pekin ducks by increasing the diversity of intestinal microbiota, enhancing the SCFAs contents, and strengthening the intestinal barrier function and immune systems. The optimal dietary supplementation dosage was recommended as 400 mg/kg in the diet.
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Affiliation(s)
- Yanhan Liu
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Y.L.); (K.A.); (X.G.)
- Shandong Provincial Center for Animal Disease Control, Ji’nan 250100, China;
| | - Cun Liu
- Shandong Provincial Center for Animal Disease Control, Ji’nan 250100, China;
| | - Keying An
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Y.L.); (K.A.); (X.G.)
| | - Xiaowei Gong
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Y.L.); (K.A.); (X.G.)
| | - Zhaofei Xia
- College of Veterinary Medicine, China Agricultural University, Beijing 100193, China; (Y.L.); (K.A.); (X.G.)
- Correspondence: ; Tel.: +86-10-62733781
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Lv M, Wang Y, Qu P, Li S, Yu Z, Qin X, Liu X. A combination of cecum microbiome and metabolome in CUMS depressed rats reveals the antidepressant mechanism of traditional Chinese medicines: A case study of Xiaoyaosan. JOURNAL OF ETHNOPHARMACOLOGY 2021; 276:114167. [PMID: 33984458 DOI: 10.1016/j.jep.2021.114167] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 04/21/2021] [Accepted: 04/24/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Xiaoyaosan (XYS), a representative and classic prescription in traditional Chinese medicines (TCMs), has been used for thousands of years for treating depression. The anti-depression effect of XYS has been demonstrated both clinically and experimentally. However, it is still unclear that whether XYS could regulate the abnormalities of gut microbiota and metabolites of cecum induced by depression, and in which way. This study aimed to explore the underlying mechanism of the anti-depressant effects of XYS from the perspective of cecal microbiota and metabolites. MATERIALS AND METHODS Chronic unpredictable mild stress (CUMS)-induced depression-like rats were used as the depression animal model. Various classic behavioral tests were performed to assess the anti-depressant effects of XYS. Additionally, the composition, the richness, and the diversity of the cecum microbiota were assessed by 16S rRNA gene sequencing technology. Besides, the metabolic profiling of cecum samples was analyzed by 1H-NMR metabolomics. Multivariate data analysis was then applied to screen the differential metabolites and to characterize the changes in cecum metabolites. Moreover, a correlation analysis between differential metabolites and crucial microbiota was conducted. RESULTS XYS significantly improved depressive behaviors and the abnormal diversity of cecum microbiota induced by CUMS. At the phylum level, XYS could significantly increase the abundance of Firmicutes while decrease the abundance of Actinobacteria in depressed rats. XYS significantly regulated the abundances of 9 out of 13 potential microbial biomarkers at the genus level. Cecal metabolomics showed that XYS could also regulate the abnormal levels of alanine, proline, lactate, and valine of depression rats. CONCLUSIONS This study revealed, for the first time, from the perspectives of microbiota and cecum metabolites, the anti-depression mechanisms of XYS. This study is of significance for not only comprehensively understanding the anti-depression effects and mechanisms of XYS, but also for providing a research approach for revealing the underlying mechanisms of action of TCMs, i.e. to apply a combination of 16S rRNA gene sequencing and metabolomics.
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Affiliation(s)
- Meng Lv
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, Taiyuan, 030006, China
| | - Yaze Wang
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, Taiyuan, 030006, China
| | - Ping Qu
- Shanxi Institute for Food and Drug Control, Taiyuan, 030001, China
| | - Shunyong Li
- School of Mathematics Sciences, Shanxi University, Taiyuan, 030006, China
| | - Zhiyi Yu
- Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Xuemei Qin
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, Taiyuan, 030006, China
| | - Xiaojie Liu
- Modern Research Center for Traditional Chinese Medicine, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan, 030006, China; Key Laboratory of Effective Substances Research and Utilization in TCM of Shanxi Province, Taiyuan, 030006, China.
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28
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Kim JY, Yi M, Kim M, Lee S, Moon HS, Yong D, Yong T. Measuring the absolute abundance of the microbiome by adding yeast containing 16S rRNA gene from a hyperthermophile. Microbiologyopen 2021; 10:e1220. [PMID: 34459541 PMCID: PMC8302012 DOI: 10.1002/mbo3.1220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 06/24/2021] [Accepted: 06/26/2021] [Indexed: 11/09/2022] Open
Abstract
High-throughput sequencing (HTS) of 16S rRNA gene amplicons provides compositional information regarding the microbial community, but not the absolute abundance of the bacteria. We aimed to develop a standardized method for quantifying the absolute abundance of bacteria in microbiome studies. To demonstrate the utility of our approach, we quantified the number of bacteria from the compositional data of the fecal and cecal microbiomes. The 16S rRNA gene of a hyperthermophile, Thermus aquaticus, was cloned into Pichia pastoris (yeast) genome, and an equivalent amount of the yeast was added to the stool and cecal samples of mice before DNA extraction. 16S rRNA gene library construction and HTS were performed after DNA extraction. The absolute abundances of bacteria were calculated using T. aquaticus reads. The average relative abundances of T. aquaticus in the five stool and five cecal samples were 0.95% and 0.33%, respectively, indicating that the number of bacteria in a cecum sample is 2.9 times higher than that in a stool sample. The method proposed for quantifying the absolute abundance of the bacterial population in this study is expected to overcome the limitation of showing only compositional data in most microbiome studies.
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Affiliation(s)
- Ju Yeong Kim
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
- Brain Korea 21 PLUS Project for Medical ScienceYonsei University College of MedicineSeoulKorea
| | - Myung‐hee Yi
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Myungjun Kim
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Seogwon Lee
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
| | - Hye Su Moon
- Department of Laboratory Medicine and Research Institute of Bacterial ResistanceYonsei University College of MedicineSeoulKorea
| | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial ResistanceYonsei University College of MedicineSeoulKorea
| | - Tai‐Soon Yong
- Department of Environmental Medical BiologyArthropods of Medical Importance Resource BankInstitute of Tropical MedicineYonsei University College of MedicineSeoulKorea
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29
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Čížková D, Ďureje Ľ, Piálek J, Kreisinger J. Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death. Heredity (Edinb) 2021; 127:141-150. [PMID: 34045683 PMCID: PMC8322053 DOI: 10.1038/s41437-021-00445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.
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Affiliation(s)
- Dagmar Čížková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- grid.4491.80000 0004 1937 116XFaculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
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Wei B, Xu QL, Zhang B, Zhou TS, Ke SZ, Wang SJ, Wu B, Xu XW, Wang H. Comparative Study of Sargassum fusiforme Polysaccharides in Regulating Cecal and Fecal Microbiota of High-Fat Diet-Fed Mice. Mar Drugs 2021; 19:364. [PMID: 34202845 PMCID: PMC8303714 DOI: 10.3390/md19070364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/07/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Seaweed polysaccharides represent a kind of novel gut microbiota regulator. The advantages and disadvantages of using cecal and fecal microbiota to represent gut microbiota have been discussed, but the regulatory effects of seaweed polysaccharides on cecal and fecal microbiota, which would benefit the study of seaweed polysaccharide-based gut microbiota regulator, have not been compared. Here, the effects of two Sargassum fusiforme polysaccharides prepared by water extraction (SfW) and acid extraction (SfA) on the cecal and fecal microbiota of high-fat diet (HFD) fed mice were investigated by 16S rRNA gene sequencing. The results indicated that 16 weeks of HFD dramatically impaired the homeostasis of both the cecal and fecal microbiota, including the dominant phyla Bacteroidetes and Actinobacteria, and genera Coriobacteriaceae, S24-7, and Ruminococcus, but did not affect the relative abundance of Firmicutes, Clostridiales, Oscillospira, and Ruminococcaceae in cecal microbiota and the Simpson's index of fecal microbiota. Co-treatments with SfW and SfA exacerbated body weight gain and partially reversed HFD-induced alterations of Clostridiales and Ruminococcaceae. Moreover, the administration of SfW and SfA also altered the abundance of genes encoding monosaccharide-transporting ATPase, α-galactosidase, β-fructofuranosidase, and β-glucosidase with the latter showing more significant potency. Our findings revealed the difference of cecal and fecal microbiota in HFD-fed mice and demonstrated that SfW and SfA could more significantly regulate the cecal microbiota and lay important foundations for the study of seaweed polysaccharide-based gut microbiota regulators.
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Affiliation(s)
- Bin Wei
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China;
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (Q.-L.X.); (B.Z.); (T.-S.Z.); (S.-Z.K.); (S.-J.W.)
| | - Qiao-Li Xu
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (Q.-L.X.); (B.Z.); (T.-S.Z.); (S.-Z.K.); (S.-J.W.)
| | - Bo Zhang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (Q.-L.X.); (B.Z.); (T.-S.Z.); (S.-Z.K.); (S.-J.W.)
| | - Tao-Shun Zhou
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (Q.-L.X.); (B.Z.); (T.-S.Z.); (S.-Z.K.); (S.-J.W.)
| | - Song-Ze Ke
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (Q.-L.X.); (B.Z.); (T.-S.Z.); (S.-Z.K.); (S.-J.W.)
| | - Si-Jia Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (Q.-L.X.); (B.Z.); (T.-S.Z.); (S.-Z.K.); (S.-J.W.)
- Center for Human Nutrition, David Geffen School of Medicine, University of California, Rehabilitation Building 32-21, 1000 Veteran Avenue, Los Angeles, CA 90024, USA
| | - Bin Wu
- Zhoushan Campus, Ocean College, Zhejiang University, Zhoushan 316021, China;
| | - Xue-Wei Xu
- Key Laboratory of Marine Ecosystem and Biogeochemistry, State Oceanic Administration & Second Institute of Oceanography, Ministry of Natural Resources, Hangzhou 310012, China;
| | - Hong Wang
- College of Pharmaceutical Science & Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, Zhejiang University of Technology, Hangzhou 310014, China; (Q.-L.X.); (B.Z.); (T.-S.Z.); (S.-Z.K.); (S.-J.W.)
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Fecal microbiota transplantation and antibiotic treatment attenuate naloxone-precipitated opioid withdrawal in morphine-dependent mice. Exp Neurol 2021; 343:113787. [PMID: 34153321 DOI: 10.1016/j.expneurol.2021.113787] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/13/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022]
Abstract
Opioid addiction can produce severe side effects including physical dependence and withdrawal. Perturbations of the gut microbiome have recently been shown to alter opioid-induced side-effects such as addiction, tolerance and dependence. In the present study, we investigated the influence of the gut microbiome on opioid withdrawal by evaluating the effects of fecal microbiota transplantation (FMT), antibiotic and probiotic treatments, and pharmacological inhibition of gut permeability in a mouse model of opioid dependence. Repeated intraperitoneal (i.p.) morphine treatment produced physical dependence that was quantified by measuring somatic signs of withdrawal (i.e. number of jumps) precipitated using the opioid antagonist naloxone. Morphine-dependent mice that received FMT from morphine-treated donor mice exhibited fewer naloxone-precipitated jumps compared to morphine-dependent counterparts receiving FMT from saline-treated donor mice. Microbial contents in the mouse cecum were altered by morphine treatment but were not differentially impacted by FMT. A broad-spectrum antibiotic cocktail (ABX) regimen reduced the bacterial load and attenuated naloxone-precipitated morphine withdrawal in morphine-dependent mice, whereas commercially available probiotic strains did not reliably alter somatic signs of opioid withdrawal. ML-7, a pharmacological inhibitor of gut permeability, reduced the morphine-induced increase in gut permeability in vivo but did not reliably alter somatic signs of naloxone-precipitated opioid withdrawal. Our results suggest that the gut microbiome impacts the development of physical dependence induced by chronic morphine administration, and that therapeutic manipulations of the gut microbiome may reduce opioid withdrawal.
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Rooney TA, Eshar D, Lee C, Weese JS. Characterization of faecal and caecal microbiota of free-ranging black-tailed prairie dogs ( Cynomys ludovicianus) using high-throughput sequencing of the V4 region of the 16S rRNA gene. CONSERVATION PHYSIOLOGY 2021; 9:coab042. [PMID: 34150210 PMCID: PMC8208658 DOI: 10.1093/conphys/coab042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 03/18/2021] [Accepted: 06/01/2021] [Indexed: 06/12/2023]
Abstract
Black-tailed prairie dogs (Cynomys ludovicianus) are keystone species within their grassland ecosystems; their population stability affects a multitude of other species. The goals of this study were to explore, describe and compare the bacterial communities in caecal and hard faecal samples from free-ranging black-tailed prairie dogs (n = 36) from KS, USA, using high-throughput sequencing of the V4 region of the 16S rRNA gene and to compare sex and geographic locations. A total of 22 paired faecal and caecal samples were collected post-mortem from free-ranging black-tailed prairie dogs from 5 different geographical locations. The results revealed that the microbiota of both faecal and caecal samples were dominated by the phylum Firmicutes (genera belonging to the Clostridiales order). There was significantly greater richness in faecal compared with caecal samples. There were significant differences between the 5 different geographic regions (P < 0.001), specifically in the relative abundances of genera. There were differences in rare members of the microbiome between faecal samples from male and female prairie dogs but with no significant impact on overall community structure. This study provides novel data and expands our knowledge about the gastrointestinal microbiome composition of free-ranging black-tailed prairie dogs, which has potential to inform conservation efforts and improve their captive management.
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Affiliation(s)
- Tess A Rooney
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - David Eshar
- Department of Clinical Sciences, College of Veterinary Medicine, Kansas State University, 1800 Denison Avenue, Manhattan, KS 66506, USA
| | - Charles Lee
- Animal Sciences and Industry, College of Agriculture, Kansas State University, 1530 Mid-Campus Drive North, Manhattan, KS 66506, USA
| | - J Scott Weese
- Ontario Veterinary College, University of Guelph, 50 Stone Road E., Guelph, Ontario N1G 2W1, Canada
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Yang T, Chakraborty S, Mandal J, Mei X, Joe B. Microbiota and Metabolites as Factors Influencing Blood Pressure Regulation. Compr Physiol 2021; 11:1731-1757. [PMID: 33792901 DOI: 10.1002/cphy.c200009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The study of microbes has rapidly expanded in recent years due to a surge in our understanding that humans host a plethora of commensal microbes, which reside in their bodies and depending upon their composition, contribute to either normal physiology or pathophysiology. This article provides a general foundation for learning about host-commensal microbial interactions as an emerging area of research. The article is divided into two sections. The first section is dedicated to introducing commensal microbiota and its known effects on the host. The second section is on metabolites, which are biochemicals that the host and the microbes use for bi-directional communication with each other. Together, the sections review what is known about how microbes interact with the host to impact cardiovascular physiology, especially blood pressure regulation. © 2021 American Physiological Society. Compr Physiol 11:1731-1757, 2021.
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Affiliation(s)
- Tao Yang
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Saroj Chakraborty
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Juthika Mandal
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Xue Mei
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
| | - Bina Joe
- Center for Hypertension and Precision Medicine and Department of Physiology and Pharmacology, University of Toledo College of Medicine and Life Sciences, Toledo, Ohio, USA
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Labarta-Bajo L, Nilsen SP, Humphrey G, Schwartz T, Sanders K, Swafford A, Knight R, Turner JR, Zúñiga EI. Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection. J Exp Med 2021; 217:152069. [PMID: 32880630 PMCID: PMC7953738 DOI: 10.1084/jem.20192276] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 06/29/2020] [Accepted: 08/06/2020] [Indexed: 12/16/2022] Open
Abstract
Intestinal barrier leakage constitutes a potential therapeutic target for many inflammatory diseases and represents a disease progression marker during chronic viral infections. However, the causes of altered gut barrier remain mostly unknown. Using murine infection with lymphocytic choriomeningitis virus, we demonstrate that, in contrast to an acute viral strain, a persistent viral isolate leads to long-term viral replication in hematopoietic and mesenchymal cells, but not epithelial cells (IECs), in the intestine. Viral persistence drove sustained intestinal epithelial barrier leakage, which was characterized by increased paracellular flux of small molecules and was associated with enhanced colitis susceptibility. Type I IFN signaling caused tight junction dysregulation in IECs, promoted gut microbiome shifts and enhanced intestinal CD8 T cell responses. Notably, both type I IFN receptor blockade and CD8 T cell depletion prevented infection-induced barrier leakage. Our study demonstrates that infection with a virus that persistently replicates in the intestinal mucosa increases epithelial barrier permeability and reveals type I IFNs and CD8 T cells as causative factors of intestinal leakage during chronic infections.
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Affiliation(s)
- Lara Labarta-Bajo
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA
| | - Steven P Nilsen
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Gregory Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Tara Schwartz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Karenina Sanders
- Department of Pediatrics, University of California, San Diego, La Jolla, CA
| | - Austin Swafford
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA.,Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA.,Department of Bioengineering, University of California, San Diego, La Jolla, CA.,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA
| | - Jerrold R Turner
- Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Elina I Zúñiga
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA
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Feng L, Zhou J, Zhang L, Liu P, Zheng P, Gao S, Song C, Yu Y, Gong Z, Wan X. Gut microbiota-mediated improvement of metabolic disorders by Qingzhuan tea in high fat diet-fed mice. J Funct Foods 2021. [DOI: 10.1016/j.jff.2021.104366] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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36
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Kahalehili HM, Newman NK, Pennington JM, Kolluri SK, Kerkvliet NI, Shulzhenko N, Morgun A, Ehrlich AK. Dietary Indole-3-Carbinol Activates AhR in the Gut, Alters Th17-Microbe Interactions, and Exacerbates Insulitis in NOD Mice. Front Immunol 2021; 11:606441. [PMID: 33552063 PMCID: PMC7858653 DOI: 10.3389/fimmu.2020.606441] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
The diet represents one environmental risk factor controlling the progression of type 1 diabetes (T1D) in genetically susceptible individuals. Consequently, understanding which specific nutritional components promote or prevent the development of disease could be used to make dietary recommendations in prediabetic individuals. In the current study, we hypothesized that the immunoregulatory phytochemcial, indole-3-carbinol (I3C) which is found in cruciferous vegetables, will regulate the progression of T1D in nonobese diabetic (NOD) mice. During digestion, I3C is metabolized into ligands for the aryl hydrocarbon receptor (AhR), a transcription factor that when systemically activated prevents T1D. In NOD mice, an I3C-supplemented diet led to strong AhR activation in the small intestine but minimal systemic AhR activity. In the absence of this systemic response, the dietary intervention led to exacerbated insulitis. Consistent with the compartmentalization of AhR activation, dietary I3C did not alter T helper cell differentiation in the spleen or pancreatic draining lymph nodes. Instead, dietary I3C increased the percentage of CD4+RORγt+Foxp3- (Th17 cells) in the lamina propria, intraepithelial layer, and Peyer's patches of the small intestine. The immune modulation in the gut was accompanied by alterations to the intestinal microbiome, with changes in bacterial communities observed within one week of I3C supplementation. A transkingdom network was generated to predict host-microbe interactions that were influenced by dietary I3C. Within the phylum Firmicutes, several genera (Intestinimonas, Ruminiclostridium 9, and unclassified Lachnospiraceae) were negatively regulated by I3C. Using AhR knockout mice, we validated that Intestinimonas is negatively regulated by AhR. I3C-mediated microbial dysbiosis was linked to increases in CD25high Th17 cells. Collectively, these data demonstrate that site of AhR activation and subsequent interactions with the host microbiome are important considerations in developing AhR-targeted interventions for T1D.
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MESH Headings
- Animals
- Bacteria/drug effects
- Bacteria/immunology
- Bacteria/metabolism
- Basic Helix-Loop-Helix Transcription Factors/agonists
- Basic Helix-Loop-Helix Transcription Factors/genetics
- Basic Helix-Loop-Helix Transcription Factors/metabolism
- Diabetes Mellitus, Type 1/chemically induced
- Diabetes Mellitus, Type 1/immunology
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 1/microbiology
- Dietary Exposure
- Disease Models, Animal
- Disease Progression
- Dysbiosis
- Gastrointestinal Microbiome/drug effects
- Host-Pathogen Interactions
- Indoles/toxicity
- Intestine, Small/drug effects
- Intestine, Small/immunology
- Intestine, Small/metabolism
- Intestine, Small/microbiology
- Mice, Inbred NOD
- Mice, Knockout
- Receptors, Aryl Hydrocarbon/agonists
- Receptors, Aryl Hydrocarbon/genetics
- Receptors, Aryl Hydrocarbon/metabolism
- Th17 Cells/drug effects
- Th17 Cells/immunology
- Th17 Cells/metabolism
- Mice
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Affiliation(s)
- Heather M. Kahalehili
- Department of Environmental Toxicology, University of California, Davis, CA, United States
| | - Nolan K. Newman
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Jamie M. Pennington
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Siva K. Kolluri
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Nancy I. Kerkvliet
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Natalia Shulzhenko
- Department of Biomedical Sciences, Oregon State University, Corvallis, OR, United States
| | - Andrey Morgun
- College of Pharmacy, Oregon State University, Corvallis, OR, United States
| | - Allison K. Ehrlich
- Department of Environmental Toxicology, University of California, Davis, CA, United States
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Liu Z, Coales I, Penney N, McDonald JAK, Phetcharaburanin J, Seyfried F, Li JV. A Subset of Roux-en-Y Gastric Bypass Bacterial Consortium Colonizes the Gut of Nonsurgical Rats without Inducing Host-Microbe Metabolic Changes. mSystems 2020; 5:e01047-20. [PMID: 33293406 PMCID: PMC8579838 DOI: 10.1128/msystems.01047-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/19/2020] [Indexed: 01/02/2023] Open
Abstract
Roux-en-Y gastric bypass (RYGB) is an effective weight loss surgery, resulting in a characteristic increase of fecal Gammaproteobacteria The contribution of this compositional change to metabolic benefits of RYGB is currently debatable. Therefore, this study employed 16S rRNA gene sequencing and metabolic profiling to monitor the dynamic colonization of the RYGB microbial consortium and their metabolic impact on the host. Eleven Wistar rats received vancomycin and enrofloxacin, followed by fecal microbiota transplantation (FMT) of cecal slurry obtained from either RYGB- or sham-operated rats. Urine and feces from the microbiota recipients (RYGB microbiota recipients [RYGBr], n = 6; sham microbiota recipients [SHAMr], n = 5) were collected pre- and post-antibiotics and 1, 3, 6, 9, and 16 days post-FMT. No significant differences in body weight and food intake were observed between RYGBr and SHAMr. While neither group reached the community richness of that of their donors, by day 6, both groups reached the richness and diversity of that prior to antibiotic treatment. However, the typical signature of RYGB microbiome-increased Enterobacteriaceae-was not replicated in these recipients after two consecutive FMT, suggesting that the environmental changes induced by the anatomical rearrangements of RYGB could be key for sustaining such a consortium. The transplanted bacteria did not induce the same metabolic signature of urine and feces as those previously reported in RYGB-operated rats. Future work is required to explore environmental factors that shape the RYGB microbiota in order to further investigate the metabolic functions of the RYGB microbiota, thereby teasing out the mechanisms of the RYGB surgery.IMPORTANCE Roux-en-Y gastric bypass (RYGB) surgery results in a long-term gut bacterial shift toward Gammaproteobacteria in both patients and rodents. The contribution of this compositional shift, or the RYGB bacterial consortium, to the metabolic benefit of the surgery remains debatable. It is unclear how well these bacteria colonize in an anatomically normal gut. This is a fundamental question in both defining the function of the RYGB microbiota and evaluating its potential as a nonsurgical treatment for obesity. We monitored the dynamic colonization of the RYGB bacterial consortium and observed that while approximately one-third of the bacterial taxa from the RYGB donor colonized in the gut of the nonoperated recipients, Gammaproteobacteria were unable to colonize for longer than 3 days. The study highlighted that a successful long-term colonization of Gammaproteobacteria-rich RYGB microbiota in nonsurgical animals requires key environmental factors that may be dictated by the intestinal anatomical modification by the surgery itself.
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Affiliation(s)
- Zhigang Liu
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Isabelle Coales
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital Campus, London, United Kingdom
| | - Nicholas Penney
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, St. Mary's Hospital Campus, London, United Kingdom
| | - Julie A K McDonald
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | | | - Florian Seyfried
- Department of General, Visceral, Transplant, Vascular, and Pediatric Surgery, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Jia V Li
- Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, Imperial College London, South Kensington Campus, London, United Kingdom
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Insects' potential: Understanding the functional role of their gut microbiome. J Pharm Biomed Anal 2020; 194:113787. [PMID: 33272789 DOI: 10.1016/j.jpba.2020.113787] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/13/2020] [Accepted: 11/17/2020] [Indexed: 12/17/2022]
Abstract
The study of insect-associated microbial communities is a field of great importance in agriculture, principally because of the role insects play as pests. In addition, there is a recent focus on the potential of the insect gut microbiome in areas such as biotechnology, given some microorganisms produce molecules with biotechnological and industrial applications, and also in biomedicine, since some bacteria and fungi are a reservoir of antibiotic resistance genes (ARGs). To date, most studies aiming to characterize the role of the gut microbiome of insects have been based on high-throughput sequencing of the 16S rRNA gene and/or metagenomics. However, recently functional approaches such as metatranscriptomics, metaproteomics and metabolomics have also been employed. Besides providing knowledge about the taxonomic distribution of microbial populations, these techniques also reveal their functional and metabolic capabilities. This information is essential to gain a better understanding of the role played by microbes comprising the microbial communities in their hosts, as well as to indicate their possible exploitation. This review provides an overview of how far we have come in characterizing insect gut functionality through omics, as well as the challenges and future perspectives in this field.
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39
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Labarta-Bajo L, Gramalla-Schmitz A, Gerner RR, Kazane KR, Humphrey G, Schwartz T, Sanders K, Swafford A, Knight R, Raffatellu M, Zúñiga EI. CD8 T cells drive anorexia, dysbiosis, and blooms of a commensal with immunosuppressive potential after viral infection. Proc Natl Acad Sci U S A 2020; 117:24998-25007. [PMID: 32958643 PMCID: PMC7547153 DOI: 10.1073/pnas.2003656117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Infections elicit immune adaptations to enable pathogen resistance and/or tolerance and are associated with compositional shifts of the intestinal microbiome. However, a comprehensive understanding of how infections with pathogens that exhibit distinct capability to spread and/or persist differentially change the microbiome, the underlying mechanisms, and the relative contribution of individual commensal species to immune cell adaptations is still lacking. Here, we discovered that mouse infection with a fast-spreading and persistent (but not a slow-spreading acute) isolate of lymphocytic choriomeningitis virus induced large-scale microbiome shifts characterized by increased Verrucomicrobia and reduced Firmicute/Bacteroidetes ratio. Remarkably, the most profound microbiome changes occurred transiently after infection with the fast-spreading persistent isolate, were uncoupled from sustained viral loads, and were instead largely caused by CD8 T cell responses and/or CD8 T cell-induced anorexia. Among the taxa enriched by infection with the fast-spreading virus, Akkermansia muciniphila, broadly regarded as a beneficial commensal, bloomed upon starvation and in a CD8 T cell-dependent manner. Strikingly, oral administration of A. muciniphila suppressed selected effector features of CD8 T cells in the context of both infections. Our findings define unique microbiome differences after chronic versus acute viral infections and identify CD8 T cell responses and downstream anorexia as driver mechanisms of microbial dysbiosis after infection with a fast-spreading virus. Our data also highlight potential context-dependent effects of probiotics and suggest a model in which changes in host behavior and downstream microbiome dysbiosis may constitute a previously unrecognized negative feedback loop that contributes to CD8 T cell adaptations after infections with fast-spreading and/or persistent pathogens.
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Affiliation(s)
- Lara Labarta-Bajo
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093
| | - Anna Gramalla-Schmitz
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093
| | - Romana R Gerner
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
- Division of Host-Microbe Systems & Therapeutics, University of California San Diego, La Jolla, CA 92093
| | - Katelynn R Kazane
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093
| | - Gregory Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
| | - Tara Schwartz
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
| | - Karenina Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
| | - Austin Swafford
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093
- Department of Computer Science & Engineering, University of California San Diego, La Jolla, CA 92093
| | - Manuela Raffatellu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093
- Division of Host-Microbe Systems & Therapeutics, University of California San Diego, La Jolla, CA 92093
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093
- Center for Mucosal Immunology, Allergy, and Vaccines, Chiba University-University of California San Diego, La Jolla, CA 92093
| | - Elina I Zúñiga
- Division of Biological Sciences, University of California San Diego, La Jolla, San Diego, CA 92093;
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40
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Effects of enzymatically modified chestnut starch on the gut microbiome, microbial metabolome, and transcriptome of diet-induced obese mice. Int J Biol Macromol 2020; 145:235-243. [DOI: 10.1016/j.ijbiomac.2019.12.169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 12/08/2019] [Accepted: 12/19/2019] [Indexed: 02/07/2023]
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Liddicoat C, Sydnor H, Cando-Dumancela C, Dresken R, Liu J, Gellie NJC, Mills JG, Young JM, Weyrich LS, Hutchinson MR, Weinstein P, Breed MF. Naturally-diverse airborne environmental microbial exposures modulate the gut microbiome and may provide anxiolytic benefits in mice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 701:134684. [PMID: 31704402 DOI: 10.1016/j.scitotenv.2019.134684] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/25/2019] [Accepted: 09/26/2019] [Indexed: 05/14/2023]
Abstract
Growing epidemiological evidence links natural green space exposure with a range of health benefits, including for mental health. Conversely, greater urbanisation associates with increased risk of mental health disorders. Microbiomes are proposed as an important but understudied link that may help explain many green space-human health associations. However, there remains a lack of controlled experimental evidence testing possible beneficial effects from passive exposure to natural biodiversity via airborne microbiota. Previous mouse model studies have used unrealistic environmental microbial exposures-including excessive soil and organic matter contact, feed supplements and injections-to demonstrate host microbiota, immune biomarker, and behavioural changes. Here, in a randomised controlled experiment, we demonstrate that realistic exposures to trace-level dust from a high biodiversity soil can change mouse gut microbiota, in comparison to dust from low biodiversity soil or no soil (control) (n = 54 total mice, comprising 3 treatments × 18 mice, with 9 females + 9 males per group). Furthermore, we found a nominal soil-derived anaerobic spore-forming butyrate-producer, Kineothrix alysoides, was supplemented to a greater extent in the gut microbiomes of high biodiversity treatment mice. Also, increasing relative abundance of this rare organism correlated with reduced anxiety-like behaviour in the most anxious mice. Our results point to an intriguing new hypothesis: that biodiverse soils may represent an important supplementary source of butyrate-producing bacteria capable of resupplying the mammalian gut microbiome, with potential for gut health and mental health benefits. Our findings have potential to inform cost-effective population health interventions through microbiome-conscious green space design and, ultimately, the mainstreaming of biodiversity into health care.
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Affiliation(s)
- Craig Liddicoat
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia.
| | - Harrison Sydnor
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Christian Cando-Dumancela
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Romy Dresken
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jiajun Liu
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Nicholas J C Gellie
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jacob G Mills
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jennifer M Young
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia; College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mark R Hutchinson
- Adelaide Medical School, The University of Adelaide, Adelaide, South Australia 5005, Australia; Australian Research Council Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Philip Weinstein
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Martin F Breed
- School of Biological Sciences and the Environment Institute, The University of Adelaide, Adelaide, South Australia 5005, Australia; College of Science and Engineering, Flinders University, Bedford Park, South Australia 5042, Australia.
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Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach. PLoS One 2019; 14:e0218143. [PMID: 31545802 PMCID: PMC6756520 DOI: 10.1371/journal.pone.0218143] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/09/2019] [Indexed: 12/16/2022] Open
Abstract
Obesity and its comorbidities are currently considered an epidemic, and the involved pathophysiology is well studied. Hypercaloric diets are tightly related to the obesity etiology and also cause alterations in gut microbiota functionality. Diet and antibiotics are known to play crucial roles in changes in the microbiota ecosystem and the disruption of its balance; therefore, the manipulation of gut microbiota may represent an accurate strategy to understand its relationship with obesity caused by diet. Fecal microbiota transplantation, during which fecal microbiota from a healthy donor is transplanted to an obese subject, has aroused interest as an effective approach for the treatment of obesity. To determine its success, a multiomics approach was used that combined metagenomics and metaproteomics to study microbiota composition and function. To do this, a study was performed in rats that evaluated the effect of a hypercaloric diet on the gut microbiota, and this was combined with antibiotic treatment to deplete the microbiota before fecal microbiota transplantation to verify its effects on gut microbiota-host homeostasis. Our results showed that a high-fat diet induces changes in microbiota biodiversity and alters its function in the host. Moreover, we found that antibiotics depleted the microbiota enough to reduce its bacterial content. Finally, we assessed the use of fecal microbiota transplantation as a complementary obesity therapy, and we found that it reversed the effects of antibiotics and reestablished the microbiota balance, which restored normal functioning and alleviated microbiota disruption. This new approach could be implemented to support the dietary and healthy habits recommended as a first option to maintain the homeostasis of the microbiota.
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Guo B, Yang B, Pang X, Chen T, Chen F, Cheng KW. Fucoxanthin modulates cecal and fecal microbiota differently based on diet. Food Funct 2019; 10:5644-5655. [PMID: 31433413 DOI: 10.1039/c9fo01018a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Obesity is a major health concern worldwide and is considered to be associated with disruption of host-microbial homeostasis, especially microbiota composition in the gastrointestinal tract. Use of microbiota-directed foods or nutraceuticals therefore represents a promising approach for the control of obesity. Fucoxanthin, a marine carotenoid, has been proven to be one of the most effective anti-obesity natural products. However, its action mechanism is yet to be unraveled, especially with respect to its role in the modulation of gut microbiota composition. In the present study, profiles of microbiota in both the cecal and fecal samples from BALB/c mice given respectively the following treatments were examined: normal chow diet (NCD), NCD + fucoxanthin (NCDF), high-fat-diet (HFD), and HFD + fucoxanthin (HFDF). The results showed that fucoxanthin supplementation for 4 weeks significantly changed the composition of both cecal and fecal microbiota. In addition, a differential effect was observed between the supplementation to NCD and to HFD. The changes in the Firmicutes/Bacteroidetes ratio and the abundance of S24-7 and Akkermansia were identified to be among the major gut microbiota modulating events associated with the anti-obesity bioactivity of fucoxanthin. Hence, our results suggested that fucoxanthin could be a promising microbiota-targeted functional-food ingredient.
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Affiliation(s)
- Bingbing Guo
- Institute for Advanced Study, Shenzhen University, Nanshan District, Shenzhen, Guangdong 518060, China. and College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China and Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Bo Yang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Xiaoyang Pang
- Institute of Agro-Food Science and Technology, Chinese Academy of Agricultural Science, Beijing, China
| | - Tianpeng Chen
- Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Feng Chen
- Institute for Advanced Study, Shenzhen University, Nanshan District, Shenzhen, Guangdong 518060, China. and Institute for Food and Bioresource Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Ka-Wing Cheng
- Institute for Advanced Study, Shenzhen University, Nanshan District, Shenzhen, Guangdong 518060, China.
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Breton J, Legrand R, Achamrah N, Chan P, do Rego JL, do Rego JC, Coëffier M, Déchelotte P, Fetissov SO. Proteome modifications of gut microbiota in mice with activity-based anorexia and starvation: Role in ATP production. Nutrition 2019; 67-68:110557. [PMID: 31563744 DOI: 10.1016/j.nut.2019.110557] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/04/2019] [Accepted: 07/04/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Activity-based anorexia (ABA) in rodents is a behavioral model of anorexia nervosa, characterized by negative energy balance, hyperactivity, and dysbiosis of gut microbiota. Gut bacteria are known to produce energy substrates including adenosine triphosphate (ATP) and acetate. The aim of this study was to determine whether ABA alters the proteome of gut microbiota relevant to ATP and acetate production. METHODS The ABA was developed in male mice and compared with food-restricted and ad libitum-fed conditions. Proteomic analysis of feces was performed using the two-dimentional gel electrophoresis and mass spectrometry. The in vitro ATP-producing capacity of proteins extracted from feces was assayed. RESULTS Increased levels of the phosphoglycerate kinase, an ATP-producing glycolytic enzyme, was detected in feces of food-restricted mice and this enzyme was further increased in the ABA group. Starvation also upregulated several other proteins synthetized by order Clostridiales including Clostridiaceae and Lachnospiraceae families. No significant differences in the in vitro ATP-producing capacity by bacterial proteins from ABA, food-restricted, and ad libitum-fed control mice were found. However, plasma levels of acetate strongly tended to be increased in the activity groups including ABA mice. CONCLUSION The data revealed that starvation in food-restricted and ABA mice induced proteome modification in gut bacteria favoring ATP production mainly by the order Clostridiales. However, this did not result in increased total ATP-production capacity by gut microbiota. These changes can be interpreted as an adaptation of specific gut bacteria to the host malnutrition beneficial for host survival.
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Affiliation(s)
- Jonathan Breton
- Normandie University, UNIROUEN, Nutrition, Gut and Brain Laboratory Rouen, France; Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France; Nutrition Department, Rouen University Hospital, Rouen, France.
| | - Romain Legrand
- Normandie University, UNIROUEN, Nutrition, Gut and Brain Laboratory Rouen, France; Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France
| | - Najate Achamrah
- Normandie University, UNIROUEN, Nutrition, Gut and Brain Laboratory Rouen, France; Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France; Nutrition Department, Rouen University Hospital, Rouen, France
| | - Philippe Chan
- Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France; Normandie University, UNIROUEN, PISSARO Proteomic Platform, Mont-Saint-Aignan, France
| | - Jean Luc do Rego
- Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France; Normandie University, UNIROUEN, Animal Behavior Platform SCAC, Rouen, France
| | - Jean Claude do Rego
- Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France; Normandie University, UNIROUEN, Animal Behavior Platform SCAC, Rouen, France
| | - Moïse Coëffier
- Normandie University, UNIROUEN, Nutrition, Gut and Brain Laboratory Rouen, France; Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France; Nutrition Department, Rouen University Hospital, Rouen, France
| | - Pierre Déchelotte
- Normandie University, UNIROUEN, Nutrition, Gut and Brain Laboratory Rouen, France; Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France; Nutrition Department, Rouen University Hospital, Rouen, France
| | - Sergueï O Fetissov
- Normandie University, UNIROUEN, Nutrition, Gut and Brain Laboratory Rouen, France; Normandie University, UNIROUEN, Institute for Research and Innovation in Biomedicine (IRIB), Rouen, France.
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45
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Abbondio M, Palomba A, Tanca A, Fraumene C, Pagnozzi D, Serra M, Marongiu F, Laconi E, Uzzau S. Fecal Metaproteomic Analysis Reveals Unique Changes of the Gut Microbiome Functions After Consumption of Sourdough Carasau Bread. Front Microbiol 2019; 10:1733. [PMID: 31417524 PMCID: PMC6682701 DOI: 10.3389/fmicb.2019.01733] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/15/2019] [Indexed: 12/29/2022] Open
Abstract
Sourdough-leavened bread (SB) is acknowledged for its great variety of valuable effects on consumer's metabolism and health, including a low glycemic index and a reduced content of the possible carcinogen acrylamide. Here, we aimed to investigate how these effects influence the gut microbiota composition and functions. Therefore, we subjected rats to a diet supplemented with SB, baker's yeast leavened bread (BB), or unsupplemented diet (chow), and, after 4 weeks of treatment, their gut microbiota was analyzed using a metaproteogenomic approach. As a result, diet supplementation with SB led to a reduction of specific members of the intestinal microbiota previously associated to low protein diets, namely Alistipes and Mucispirillum, or known as intestinal pathobionts, i.e., Mycoplasma. Concerning functions, asparaginases expressed by Bacteroides were observed as more abundant in SB-fed rats, leading to hypothesize that in their colonic microbiota the enzyme substrate, asparagine, was available in higher amounts than in BB- and chow-fed rats. Another group of protein families, expressed by Clostridium, was detected as more abundant in animal fed SB-supplemented diet. Of these, manganese catalase, small acid-soluble proteins (SASP), Ser/Thr kinase PrkA, and V-ATPase proteolipid subunit have been all reported to take part in Clostridium sporulation, strongly suggesting that the diet supplementation with SB might promote environmental conditions inducing metabolic dormancy of Clostridium spp. within the gut microbiota. In conclusion, our data describe the effects of SB consumption on the intestinal microbiota taxonomy and functions in rats. Moreover, our results suggest that a metaproteogenomic approach can provide evidence of the interplay between metabolites deriving from bread digestion and microbial metabolism.
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Affiliation(s)
- Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Antonio Palomba
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Alghero, Italy
| | - Alessandro Tanca
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Alghero, Italy
| | - Cristina Fraumene
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Alghero, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, Science and Technology Park of Sardinia, Alghero, Italy
| | - Monica Serra
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Fabio Marongiu
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Ezio Laconi
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Porto Conte Ricerche, Science and Technology Park of Sardinia, Alghero, Italy
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46
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Vemuri R, Gundamaraju R, Shinde T, Perera AP, Basheer W, Southam B, Gondalia SV, Karpe AV, Beale DJ, Tristram S, Ahuja KDK, Ball M, Martoni CJ, Eri R. Lactobacillus acidophilus DDS-1 Modulates Intestinal-Specific Microbiota, Short-Chain Fatty Acid and Immunological Profiles in Aging Mice. Nutrients 2019; 11:E1297. [PMID: 31181695 PMCID: PMC6627711 DOI: 10.3390/nu11061297] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023] Open
Abstract
Distribution of the microbiota varies according to the location in the gastrointestinal (GI) tract. Thus, dysbiosis during aging may not be limited to faecal microbiota and extend to the other parts of the GI tract, especially the cecum and colon. Lactobacillus acidophilus DDS-1, a probiotic strain, has been shown to modulate faecal microbiota and its associated metabolic phenotype in aging mice. In the present study, we investigated the effect of L. acidophilus DDS-1 supplementation on caecal- and mucosal-associated microbiota, short-chain fatty acids (SCFAs) and immunological profiles in young and aging C57BL/6J mice. Besides differences in the young and aging control groups, we observed microbial shifts in caecal and mucosal samples, leading to an alteration in SCFA levels and immune response. DDS-1 treatment increased the abundances of beneficial bacteria such as Akkermansia spp. and Lactobacillus spp. more effectively in caecal samples than in mucosal samples. DDS-1 also enhanced the levels of butyrate, while downregulating the production of inflammatory cytokines (IL-6, IL-1β, IL-1α, MCP-1, MIP-1α, MIP-1β, IL-12 and IFN-γ) in serum and colonic explants. Our findings suggest distinct patterns of intestinal microbiota, improvements in SCFA and immunological profiles with DDS-1 supplementation in aging mice.
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Affiliation(s)
- Ravichandra Vemuri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Rohit Gundamaraju
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Tanvi Shinde
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
- Centre for Food Safety and Innovation, Tasmanian Institute of Agriculture, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Agampodi Promoda Perera
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Waheedha Basheer
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Benjamin Southam
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Shakuntla V Gondalia
- Centre for Human Psychopharmacology, Swinburne University of Technology, Hawthorn, Victoria, 3122, Australia.
| | - Avinash V Karpe
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, Queensland, 4102, Australia.
| | - David J Beale
- Land and Water, Commonwealth Scientific and Industrial Research Organization (CSIRO), Ecosciences Precinct, Dutton Park, Queensland, 4102, Australia.
| | - Stephen Tristram
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Kiran D K Ahuja
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
| | - Madeleine Ball
- School of Health and Biomedical Sciences, RMIT University, Bundoora, Victoria, 3082 Australia.
| | | | - Rajaraman Eri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston, Tasmania, 7250 Australia.
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Panebianco C, Pazienza V. Body site-dependent variations of microbiota in pancreatic cancer pathophysiology. Crit Rev Clin Lab Sci 2019; 56:260-273. [PMID: 31060399 DOI: 10.1080/10408363.2019.1615407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Lack of specific symptoms and reliable biomarkers, along with aggressive nature and resistance to therapies makes pancreatic cancer (PC) one of the leading causes of death from cancer worldwide. The search for new diagnostic, prognostic, predictive, and therapeutic tools that could improve clinical outcomes of patients has led, in recent years, to the investigation of potential roles for the microbiota in the pathogenesis of this disease. The human microbiota encompasses trillions of microorganisms residing within several body tissues and organs, where they provide beneficial functions for host homeostasis and health. Derangements of the microbial ecology in different anatomic districts have been described in PC, as in many other diseases, both in patients and in animal models. In detail, infection from the gastric pathogen Helicobacter pylori and changes in composition and diversity of oral, intestinal, and pancreatic microbiota have been found to associate with PC. Future research should assess how to potentially exploit such differences in microbiota composition as diagnostic, prognostic, or predictive biomarkers, and as targets for therapeutic interventions, in the hope of improving the dismal prognosis of this insidious cancer.
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Affiliation(s)
- Concetta Panebianco
- a Division of Gastroenterology , Fondazione IRCCS Casa Sollievo della Sofferenza , San Giovanni Rotondo , Italy
| | - Valerio Pazienza
- a Division of Gastroenterology , Fondazione IRCCS Casa Sollievo della Sofferenza , San Giovanni Rotondo , Italy
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48
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Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Rev Proteomics 2019; 16:375-390. [PMID: 31002542 DOI: 10.1080/14789450.2019.1609944] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The study of microbial communities based on the combined analysis of genomic and proteomic data - called metaproteogenomics - has gained increased research attention in recent years. This relatively young field aims to elucidate the functional and taxonomic interplay of proteins in microbiomes and its implications on human health and the environment. Areas covered: This article reviews bioinformatics methods and software tools dedicated to the analysis of data from metaproteomics and metaproteogenomics experiments. In particular, it focuses on the creation of tailored protein sequence databases, on the optimal use of database search algorithms including methods of error rate estimation, and finally on taxonomic and functional annotation of peptide and protein identifications. Expert opinion: Recently, various promising strategies and software tools have been proposed for handling typical data analysis issues in metaproteomics. However, severe challenges remain that are highlighted and discussed in this article; these include: (i) robust false-positive assessment of peptide and protein identifications, (ii) complex protein inference against a background of highly redundant data, (iii) taxonomic and functional post-processing of identification data, and finally, (iv) the assessment and provision of metrics and tools for quantitative analysis.
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Affiliation(s)
- Henning Schiebenhoefer
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Tim Van Den Bossche
- b VIB - UGent Center for Medical Biotechnology, VIB , Ghent , Belgium.,c Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
| | - Stephan Fuchs
- d FG13 Division of Nosocomial Pathogens and Antibiotic Resistances , Robert Koch Institute , Wernigerode , Germany
| | - Bernhard Y Renard
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Thilo Muth
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Lennart Martens
- b VIB - UGent Center for Medical Biotechnology, VIB , Ghent , Belgium.,c Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
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49
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Abstract
The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.
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Affiliation(s)
- Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine , University of Ottawa , Ottawa , Ontario K1H 8M5 , Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine , University of Ottawa , Ottawa , Ontario K1H 8M5 , Canada
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50
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Zeng Y, Zhang J, Zhang Y, Men Y, Zhang B, Sun Y. Prebiotic, Immunomodulating, and Antifatigue Effects of Konjac Oligosaccharide. J Food Sci 2018; 83:3110-3117. [PMID: 30511769 DOI: 10.1111/1750-3841.14376] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 09/10/2018] [Accepted: 09/15/2018] [Indexed: 01/26/2023]
Abstract
Irregular and long time work schedules not only makes people feel fatigue, but also brings great risks of diseases, due to gastrointestinal disorder and immune dysfunction. Therefore, it has positive significance to help challenged people stay energetic and healthy with food supplement. Konjac oligosaccharide has shown various physiological benefits and been recommended in the fortification of functional foods. However, there have been few reports on its application aimed to simultaneously relieve physical fatigue and keep body healthy. In this paper, the potential prebiotic, immunoregulatory, and antifatigue activities of konjac oligosaccharide were evaluated in vitro and in vivo. The results showed that konjac oligosaccharide could promote probiotics growth and short chain fatty acids production in mice cecum. At the concentration of 50 to 200 μg/mL, konjac oligosaccharide could activate murine macrophage RAW 264.7 to secret NO and cytokines of IL-10 and IL-6. Moreover, this oligosaccharide could alleviate physical fatigue by prolonging exhaustive time, improving the level of superoxide dismutases and glutathione peroxidase, increasing the content of blood glucose, and decreasing the content of blood urea nitrogen. The results suggested that konjac oligosaccharide had prebiotic, immunoregulatory, and antifatigue effects, providing its application potential in functional food aimed at people with irregular and long time work.
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Affiliation(s)
- Yan Zeng
- Natl. Engineering Laboratory for Industrial Enzymes, Tianjin Inst. of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Jiangang Zhang
- Natl. Engineering Laboratory for Industrial Enzymes, Tianjin Inst. of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Ying Zhang
- Natl. Engineering Laboratory for Industrial Enzymes, Tianjin Inst. of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Yan Men
- Natl. Engineering Laboratory for Industrial Enzymes, Tianjin Inst. of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Bo Zhang
- Key Laboratory for Bioactive Material and Functional Food of Beijing, College of Biochemical Engineering, Beijing Union Univ., Beijing, 100023, China
| | - Yuanxia Sun
- Natl. Engineering Laboratory for Industrial Enzymes, Tianjin Inst. of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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