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Piazzesi A, Pane S, Romani L, Toto F, Scanu M, Marsiglia R, Del Chierico F, Cotugno N, Palma P, Putignani L. Gut Microbial Signatures Associated with Cryptosporidiosis: A Case Series. Microorganisms 2025; 13:342. [PMID: 40005709 PMCID: PMC11858469 DOI: 10.3390/microorganisms13020342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2024] [Revised: 01/24/2025] [Accepted: 01/26/2025] [Indexed: 02/27/2025] Open
Abstract
Cryptosporidium spp. are zoonotic protozoan parasites with a global prevalence, with both gastrointestinal and pulmonary involvement. Though symptoms can often be relatively mild, they can become severe and even fatal in children under five, the elderly, and in immunocompromised individuals, making cryptosporidiosis a leading cause of morbidity and mortality in fragile populations. Furthermore, there is an urgent clinical need for alternative therapies against cryptosporidiosis, as currently available FDA-approved treatments are ineffective in the immunocompromised. Recent evidence in animal models suggests that the gut microbiota (GM) can influence both host and parasite biology to influence the course of Cryptosporidium infection. Here, we present GM profiles in five cases of cryptosporidiosis, associated with varying underlying pathologies. We found that moderate-severe cryptosporidiosis was characterized by a reduction in alpha-diversity and an enrichment of Enterococcus spp., while decreases in Bifidobacterium, Gemmiger, and Blautia were detectable in the milder manifestations of the disease. Our results suggest that severe cryptosporidiosis is associated with a stronger change on the GM than is age or underlying pathology. Together with previously published studies in animal models, we believe that these results suggest that the GM could be a potential therapeutic target for human patients as well, particularly in the immunocompromised for whom anti-Cryptosporidium treatment remains largely ineffective.
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Affiliation(s)
- Antonia Piazzesi
- Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (A.P.); (F.T.); (M.S.); (R.M.); (F.D.C.)
| | - Stefania Pane
- Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy;
| | - Lorenza Romani
- Infectious Diseases Unit, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy;
| | - Francesca Toto
- Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (A.P.); (F.T.); (M.S.); (R.M.); (F.D.C.)
| | - Matteo Scanu
- Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (A.P.); (F.T.); (M.S.); (R.M.); (F.D.C.)
| | - Riccardo Marsiglia
- Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (A.P.); (F.T.); (M.S.); (R.M.); (F.D.C.)
| | - Federica Del Chierico
- Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (A.P.); (F.T.); (M.S.); (R.M.); (F.D.C.)
| | - Nicola Cotugno
- Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (N.C.); (P.P.)
| | - Paolo Palma
- Unit of Clinical Immunology and Vaccinology, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (N.C.); (P.P.)
- Department of Systems Medicine, University of Rome “Tor Vergata”, 00133 Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiology and Diagnostic Immunology, Unit of Microbiomics and Management and Diagnostic Innovations & Clinical Pathways Research Area, Unit of Microbiome, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy
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Marzano V, Levi Mortera S, Putignani L. Insights on Wet and Dry Workflows for Human Gut Metaproteomics. Proteomics 2024:e202400242. [PMID: 39740098 DOI: 10.1002/pmic.202400242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 12/10/2024] [Accepted: 12/11/2024] [Indexed: 01/02/2025]
Abstract
The human gut microbiota (GM) is a community of microorganisms that resides in the gastrointestinal (GI) tract. Recognized as a critical element of human health, the functions of the GM extend beyond GI well-being to influence overall systemic health and susceptibility to disease. Among the other omic sciences, metaproteomics highlights additional facets that make it a highly valuable discipline in the study of GM. Indeed, it allows the protein inventory of complex microbial communities. Proteins with associated taxonomic membership and function are identified and quantified from their constituent peptides by liquid chromatography coupled to mass spectrometry analyses and by querying specific databases (DBs). The aim of this review was to compile comprehensive information on metaproteomic studies of the human GM, with a focus on the bacterial component, to assist newcomers in understanding the methods and types of research conducted in this field. The review outlines key steps in a metaproteomic-based study, such as protein extraction, DB selection, and bioinformatic workflow. The importance of standardization is emphasized. In addition, a list of previously published studies is provided as hints for researchers interested in investigating the role of GM in health and disease states.
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Affiliation(s)
- Valeria Marzano
- Research Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Stefano Levi Mortera
- Research Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Lorenza Putignani
- Unit of Microbiomics and Research Unit of Microbiome, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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Trivedi A, Bose D, Moffat K, Pearson E, Walsh D, Cohen D, Skupsky J, Chao L, Golier J, Janulewicz P, Sullivan K, Krengel M, Tuteja A, Klimas N, Chatterjee S. Gulf War Illness Is Associated with Host Gut Microbiome Dysbiosis and Is Linked to Altered Species Abundance in Veterans from the BBRAIN Cohort. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2024; 21:1102. [PMID: 39200711 PMCID: PMC11354743 DOI: 10.3390/ijerph21081102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 08/09/2024] [Accepted: 08/13/2024] [Indexed: 09/02/2024]
Abstract
Gulf War Illness (GWI) is a debilitating condition marked by chronic fatigue, cognitive problems, pain, and gastrointestinal (GI) complaints in veterans who were deployed to the 1990-1991 Gulf War. Fatigue, GI complaints, and other chronic symptoms continue to persist more than 30 years post-deployment. Several potential mechanisms for the persistent illness have been identified and our prior pilot study linked an altered gut microbiome with the disorder. This study further validates and builds on our prior preliminary findings of host gut microbiome dysbiosis in veterans with GWI. Using stool samples and Multidimensional Fatigue Inventory (MFI) data from 89 GW veteran participants (63 GWI cases and 26 controls) from the Boston biorepository, recruitment, and integrative network (BBRAIN) for Gulf War Illness, we found that the host gut bacterial signature of veterans with GWI showed significantly different Bray-Curtis beta diversity than control veterans. Specifically, a higher Firmicutes to Bacteroidetes ratio, decrease in Akkermansia sp., Bacteroides thetaiotamicron, Bacteroides fragilis, and Lachnospiraceae genera and increase in Blautia, Streptococcus, Klebsiella, and Clostridium genera, that are associated with gut, immune, and brain health, were shown. Further, using MaAsLin and Boruta algorithms, Coprococcus and Eisenbergiella were identified as important predictors of GWI with an area under the curve ROC predictive value of 74.8%. Higher self-reported MFI scores in veterans with GWI were also significantly associated with an altered gut bacterial diversity and species abundance of Lachnospiraceae and Blautia. These results suggest potential therapeutic targets for veterans with GWI that target the gut microbiome and specific symptoms of the illness.
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Affiliation(s)
- Ayushi Trivedi
- Environmental Health and Disease Laboratory, Department of Environmental and Occupational Health, Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA; (A.T.); (D.B.)
| | - Dipro Bose
- Environmental Health and Disease Laboratory, Department of Environmental and Occupational Health, Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA; (A.T.); (D.B.)
| | - Kelly Moffat
- CosmosID, Germantown, MD 20874, USA; (K.M.); (D.W.)
| | | | - Dana Walsh
- CosmosID, Germantown, MD 20874, USA; (K.M.); (D.W.)
| | - Devra Cohen
- Miami VA Healthcare System, Miami, FL 33125, USA;
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
| | - Jonathan Skupsky
- VA Research and Development, VA Long Beach Health Care, Long Beach, CA 90822, USA;
| | - Linda Chao
- San Francisco Veterans Affairs Health Care System, San Francisco, CA 94121, USA
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94143, USA
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA 94143, USA
| | - Julia Golier
- J. Peters VA Medical Center, Bronx, NY 10468, USA;
- Psychiatry Department, Icahn School of Medicine at Mount Sinai, 1428 Madison Ave, New York, NY 10029, USA
| | - Patricia Janulewicz
- Department of Environmental Health, Boston University School of Public Health, 715 Albany St. T4W, Boston, MA 02130, USA; (P.J.)
| | - Kimberly Sullivan
- Department of Environmental Health, Boston University School of Public Health, 715 Albany St. T4W, Boston, MA 02130, USA; (P.J.)
| | - Maxine Krengel
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02130, USA;
| | - Ashok Tuteja
- Division of Gastroenterology, School of Medicine, University of Utah, Salt Lake City, UT 84132, USA;
| | - Nancy Klimas
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
- Geriatric Research and Education Clinical Center, Miami VA Heathcare System, Miami, FL 33125, USA
| | - Saurabh Chatterjee
- Environmental Health and Disease Laboratory, Department of Environmental and Occupational Health, Program in Public Health, Susan and Henry Samueli College of Health Sciences, University of California, Irvine, CA 92697, USA; (A.T.); (D.B.)
- Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, FL 33314, USA;
- Department of Medicine, Infectious Disease, UCI School of Medicine, Irvine, CA 92697, USA
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Wang N, Li Z, Cao L, Cui Z. Trilobatin ameliorates dextran sulfate sodium-induced ulcerative colitis in mice via the NF-κB pathway and alterations in gut microbiota. PLoS One 2024; 19:e0305926. [PMID: 38913606 PMCID: PMC11195961 DOI: 10.1371/journal.pone.0305926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/06/2024] [Indexed: 06/26/2024] Open
Abstract
OBJECTIVE This study aimed to evaluate the effects of trilobatin (TLB) on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) in mice and further explore the underlying mechanisms from the perspectives of signaling pathway and gut microbiota. METHODS A mouse model of UC was established using DSS. Trilobatin was administered via oral gavage. Disease severity was assessed based on body weight, disease activity index (DAI), colon length, histological detection, inflammation markers, and colonic mucosal barrier damage. Alternations in the NF-κB and PI3K/Akt pathways were detected by marker proteins. High-throughput 16S rRNA sequencing was performed to investigate the gut microbiota of mice. RESULTS In the DSS-induced UC mice, TLB (30 μg/g) treatment significantly increased the body weight, reduced the DAI score, alleviated colon length shortening, improved histopathological changes in colon tissue, inhibited the secretion and expression of inflammation factors (TNF-α, IL-1β, and IL-6), and increased the expression of tight-junction proteins (ZO-1 and occludin). Furthermore, TLB (30 μg/g) treatment significantly suppressed the activation of NF-κB pathway and altered the composition and diversity of the gut microbiota, as observed in the variations of the relative abundances of Proteobacteria, Actinobacteriota, and Bacteroidota, in UC mice. CONCLUSION TLB effectively alleviates DSS-induced UC in mice. Regulation of the NF-κB pathway and gut microbiota contributes to TLB-mediated therapeutic effects. Our study not only identified a novel drug candidate for the treatment of UC, but also enhanced our understanding of the biological functions of TLB.
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Affiliation(s)
- Nanbo Wang
- Department of Gastric and Colorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Zhaohui Li
- Changchun People’s Hospital of Jilin Province, Changchun, China
| | - Lingling Cao
- School of Clinical Medical, Changchun University of Chinese Medicine, Changchun, China
| | - Zhihua Cui
- The First Hospital of Jilin University, Changchun, China
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Dahab M, Idris H, Zhang P, Aladhadh M, Alatawi EA, Ming LC, Goh KW, Ser HL. Influence of Maqian essential oil on gut microbiota and immunoresponses in type 1 diabetes: In silico study. Heliyon 2024; 10:e29490. [PMID: 38655301 PMCID: PMC11035065 DOI: 10.1016/j.heliyon.2024.e29490] [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: 01/01/2024] [Revised: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024] Open
Abstract
Diversity and homeostasis of gut bacterial composition is highly associated with the pathogenesis of insulin dysfunction and type 1 diabetes melittus (T1D), hence emerged in parallel with the activation of autoimmunity. We aimed to study the bioactive potential of essential oil from Zanthoxylum myriacanthum var. pubescens Huang (Maqian) through computational approaches. Twelve chemical constituents derived from Maqian essential oil were docked with selected proteins (i.e., 3pig, 1kho, 7dmq, 4m4d, 2z65, 4glp, and 3fxi) in which are involved in gut microbiota modulation in T1D. Subsequently, the prediction of bioavailability properties of the small molecules were evaluated. Among all chemical constituents, the post-docking interaction analysis demonstrated that α-phellandrene exhibits the strongest binding affinity and induces gut microbiota modulation with β-fructofuranosidase from Bifidobacterium longum. The current result revealed the potential of 3-Carene and α-Pinene in inducing specific changes in gut microbiota downregulating Clostridium perfringens and quenching Leptotrichia shahii respectively. β-Pinene possess exceptionally strong binding affinity that effectively disrupt the interaction between lipopolysaccharide and its cognate receptors, while α-Phellandrene was exhibited the uppermost binding affinity with TLR4/MD2 and could likely target TLR4 stimulating lipopolysaccharide. Our results are the first to report on the gut microbiota modulation effects of α-Phellandrene and β-Phellandrene via actions on LPS binding to CD14 and the TLR4 co-receptor signaling. In conclusion, our findings based on computational approaches, small molecules from Maqian present as promising agents which could regulate inflammatory response and modulate gut microbiota in type 1 diabetes mellitus.
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Affiliation(s)
- Mahmoud Dahab
- Department of Microbiology, Faculty of Pure and Applied Sciences, International University of Africa, P.O. Box 2469, Khartoum, Sudan
| | - Hajo Idris
- Department of Physics, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, 11623, Saudi Arabia
| | - Ping Zhang
- Center for Integrative Conservation, Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China
| | - Mohammed Aladhadh
- Department of Food Science and Human Nutrition, College of Agriculture and Food, Qassim University, Buraydah 51452, Saudi Arabia
| | - Eid A Alatawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, University of Tabuk, 71491, Saudi Arabia
| | - Long Chiau Ming
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, Sunway City 47500, Malaysia
| | - Khang Wen Goh
- Faculty of Data Science and Information Technology, INTI International University, Nilai, Malaysia
| | - Hooi-Leng Ser
- Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, Sunway City, 47500, Malaysia
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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 CACTUS Study Team. 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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