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Fekete EE, Figeys D, Zhang X. Microbiota-directed biotherapeutics: considerations for quality and functional assessment. Gut Microbes 2023; 15:2186671. [PMID: 36896938 PMCID: PMC10012963 DOI: 10.1080/19490976.2023.2186671] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/11/2023] Open
Abstract
Mounting evidence points to causative or correlative roles of gut microbiome in the development of a myriad of diseases ranging from gastrointestinal diseases, metabolic diseases to neurological disorders and cancers. Consequently, efforts have been made to develop and apply therapeutics targeting the human microbiome, in particular the gut microbiota, for treating diseases and maintaining wellness. Here we summarize the current development of gut microbiota-directed therapeutics with a focus on novel biotherapeutics, elaborate the need of advanced -omics approaches for evaluating the microbiota-type biotherapeutics, and discuss the clinical and regulatory challenges. We also discuss the development and potential application of ex vivo microbiome assays and in vitro intestinal cellular models in this context. Altogether, this review aims to provide a broad view of promises and challenges of the emerging field of microbiome-directed human healthcare.
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Affiliation(s)
- Emily Ef Fekete
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada.,Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Xu Zhang
- Regulatory Research Division, Centre for Oncology, Radiopharmaceuticals and Research, Biologic and Radiopharmaceutical Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Canada.,School of Pharmaceutical Sciences, Faculty of Medicine, University of Ottawa, Ottawa, Canada
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52
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Simon MC, Sina C, Ferrario PG, Daniel H. Gut Microbiome Analysis for Personalized Nutrition: The State of Science. Mol Nutr Food Res 2023; 67:e2200476. [PMID: 36424179 DOI: 10.1002/mnfr.202200476] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/17/2022] [Indexed: 11/27/2022]
Abstract
Whereas most concepts of personalized nutrition (PN) in the past, included genotyping, recent years have brought new approaches that include microbiome analysis to optimize recommendations for diet and lifestyle changes. The new approach, offered by companies, that microbiome analysis provides a real benefit to either more concise recommendations or for increased compliance to PN, is largely lacking scientific validation. Although the microbiome field shows enormous proliferation, it has some major flaws that make its use in the public health domain currently critical. Starting with the quality and representative character of the stool samples, its processing and analysis as well as assembly of metagenome data and the interpretation. Moreover, there is still no consensus of what constitutes a "normal/healthy" microbiome, nor what features characterize a dysbiotic microbiome. And, based on hundreds of individual parameters and environmental factors, the intestinal microbiome shows a huge variability and consequently changing one factor-such as food intake-is likely to have a limited impact in achieving optimized health. The present review intends to summarize the state of consolidated knowledge on human gut microbiome in the context of diet and disease, its key features, and its influencing factors as well as its "add-on" quality for PN offers.
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Affiliation(s)
- Marie-Christine Simon
- Department of Nutrition and Food Science, Nutrition and Microbiome, University of Bonn, 53115, Bonn, Germany
| | - Christian Sina
- Institute of Nutritional Medicine, University Hospital Schleswig-Holstein, 23538, Campus Lübeck, Germany
| | - Paola G Ferrario
- Department of Physiology and Biochemistry of Nutrition, Max Rubner-Institut, 76131, Karlsruhe, Germany
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- Department of Nutrition and Food Science, Nutrition and Microbiome, University of Bonn, 53115, Bonn, Germany
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53
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Kawalec A, Kiliś-Pstrusińska K. Gut Microbiota Alterations and Primary Glomerulonephritis in Children: A Review. Int J Mol Sci 2022; 24:ijms24010574. [PMID: 36614013 PMCID: PMC9820462 DOI: 10.3390/ijms24010574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/20/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
The article summarizes the current evidence on the impact of microbiota alterations on immune-mediated primary glomerulonephritis in children. In particular, the focus is on the link between dysbiosis and the onset or recurrence of idiopathic nephrotic syndrome, immunoglobulin A nephropathy, and membranous nephropathy. The aim is to describe possible pathomechanisms, differences in gut microbiota composition between pediatric patients and healthy controls, and possible usage of microbiota manipulations in supportive therapy. On this basis, we attempt to indicate directions for further research in that field.
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Interdisciplinary Overview of Lipopeptide and Protein-Containing Biosurfactants. Genes (Basel) 2022; 14:genes14010076. [PMID: 36672817 PMCID: PMC9859011 DOI: 10.3390/genes14010076] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
Biosurfactants are amphipathic molecules capable of lowering interfacial and superficial tensions. Produced by living organisms, these compounds act the same as chemical surfactants but with a series of improvements, the most notable being biodegradability. Biosurfactants have a wide diversity of categories. Within these, lipopeptides are some of the more abundant and widely known. Protein-containing biosurfactants are much less studied and could be an interesting and valuable alternative. The harsh temperature, pH, and salinity conditions that target organisms can sustain need to be understood for better implementation. Here, we will explore biotechnological applications via lipopeptide and protein-containing biosurfactants. Also, we discuss their natural role and the organisms that produce them, taking a glimpse into the possibilities of research via meta-omics and machine learning.
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Conti G, D’Amico F, Fabbrini M, Brigidi P, Barone M, Turroni S. Pharmacomicrobiomics in Anticancer Therapies: Why the Gut Microbiota Should Be Pointed Out. Genes (Basel) 2022; 14:55. [PMID: 36672796 PMCID: PMC9859289 DOI: 10.3390/genes14010055] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/09/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Anticancer treatments have shown a variable therapeutic outcome that may be partly attributable to the activity of the gut microbiota on the pathology and/or therapies. In recent years, microbiota-drug interactions have been extensively investigated, but most of the underlying molecular mechanisms still remain unclear. In this review, we discuss the relationship between the gut microbiota and some of the most commonly used drugs in oncological diseases. Different strategies for manipulating the gut microbiota layout (i.e., prebiotics, probiotics, antibiotics, and fecal microbiota transplantation) are then explored in order to optimize clinical outcomes in cancer patients. Anticancer technologies that exploit tumor-associated bacteria to target tumors and biotransform drugs are also briefly discussed. In the field of pharmacomicrobiomics, multi-omics strategies coupled with machine and deep learning are urgently needed to bring to light the interaction among gut microbiota, drugs, and host for the development of truly personalized precision therapies.
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Affiliation(s)
- Gabriele Conti
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Federica D’Amico
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Marco Fabbrini
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Patrizia Brigidi
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
| | - Monica Barone
- Microbiomics Unit, Department of Medical and Surgical Sciences, University of Bologna, 40138 Bologna, Italy
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Silvia Turroni
- Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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Saralegui C, García-Durán C, Romeu E, Hernáez-Sánchez ML, Maruri A, Bastón-Paz N, Lamas A, Vicente S, Pérez-Ruiz E, Delgado I, Luna-Paredes C, Caballero JDD, Zamora J, Monteoliva L, Gil C, del Campo R. Statistical Evaluation of Metaproteomics and 16S rRNA Amplicon Sequencing Techniques for Study of Gut Microbiota Establishment in Infants with Cystic Fibrosis. Microbiol Spectr 2022; 10:e0146622. [PMID: 36255300 PMCID: PMC9784762 DOI: 10.1128/spectrum.01466-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/23/2022] [Indexed: 01/05/2023] Open
Abstract
Newborn screening for cystic fibrosis (CF) can identify affected but asymptomatic infants. The selection of omic technique for gut microbiota study is crucial due to both the small amount of feces available and the low microorganism load. Our aims were to compare the agreement between 16S rRNA amplicon sequencing and metaproteomics by a robust statistical analysis, including both presence and abundance of taxa, to describe the sequential establishment of the gut microbiota during the first year of life in a small size sample (8 infants and 28 fecal samples). The taxonomic assignations by the two techniques were similar, whereas certain discrepancies were observed in the abundance detection, mostly the lower predicted relative abundance of Bifidobacterium and the higher predicted relative abundance of certain Firmicutes and Proteobacteria by amplicon sequencing. During the first months of life, the CF gut microbiota is characterized by a significant enrichment of Ruminococcus gnavus, the expression of certain virulent bacterial traits, and the detection of human inflammation-related proteins. Metaproteomics provides information on composition and functionality, as well as data on host-microbiome interactions. Its strength is the identification and quantification of Actinobacteria and certain classes of Firmicutes, but alpha diversity indices are not comparable to those of amplicon sequencing. Both techniques detected an aberrant microbiota in our small cohort of infants with CF during their first year of life, dominated by the enrichment of R. gnavus within a human inflammatory environment. IMPORTANCE In recent years, some techniques have been incorporated for the study of microbial ecosystems, being 16S rRNA gene sequencing being the most widely used. Metaproteomics provides the advantage of identifying the interaction between microorganisms and human cells, but the available databases are less extensive as well as imprecise. Few studies compare the statistical differences between the two techniques to define the composition of an ecosystem. Our work shows that the two methods are comparable in terms of microorganism identification but provide different results in alpha diversity analysis. On the other hand, we have studied newborns with cystic fibrosis, for whom we have described the establishment of an intestinal ecosystem marked by the inflammatory response of the host and the enrichment of Ruminococcus gnavus.
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Affiliation(s)
- Claudia Saralegui
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Carmen García-Durán
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Eduardo Romeu
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Ainhize Maruri
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Natalia Bastón-Paz
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Adelaida Lamas
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Saioa Vicente
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Servicio de Pediatría, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
| | - Estela Pérez-Ruiz
- Unidad de Fibrosis Quística, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Isabel Delgado
- Unidad de Fibrosis Quística, Hospital Virgen del Rocío, Seville, Spain
| | - Carmen Luna-Paredes
- Sección de Neumología y Alergia Infantil, Unidad Multidisciplinar Fibrosis Quística, Hospital Doce de Octubre, Madrid, Spain
| | - Juan de Dios Caballero
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Javier Zamora
- Unidad de Bioestadística, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria and CIBERESP, Madrid, Spain
| | - Lucía Monteoliva
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Concepción Gil
- Departamento de Microbiología y Parasitología, Universidad Complutense de Madrid and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- Unidad de Proteómica, Universidad Complutense de Madrid, Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria, Madrid, Spain
- CIBERINFEC, Madrid, Spain
- Unidad de Fibrosis Quística, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Universidad Alfonso X El Sabio, Madrid, Spain
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Huang Z, Liu K, Ma W, Li D, Mo T, Liu Q. The gut microbiome in human health and disease-Where are we and where are we going? A bibliometric analysis. Front Microbiol 2022; 13:1018594. [PMID: 36590421 PMCID: PMC9797740 DOI: 10.3389/fmicb.2022.1018594] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022] Open
Abstract
Background There are trillions of microbiota in our intestinal tract, and they play a significant role in health and disease via interacting with the host in metabolic, immune, neural, and endocrine pathways. Over the past decades, numerous studies have been published in the field of gut microbiome and disease. Although there are narrative reviews of gut microbiome and certain diseases, the whole field is lack of systematic and quantitative analysis. Therefore, we outline research status of the gut microbiome and disease, and present insights into developments and characteristics of this field to provide a holistic grasp and future research directions. Methods An advanced search was carried out in the Web of Science Core Collection (WoSCC), basing on the term "gut microbiome" and its synonyms. The current status and developing trends of this scientific domain were evaluated by bibliometric methodology. CiteSpace was used to perform collaboration network analysis, co-citation analysis and citation burst detection. Results A total of 29,870 articles and 13,311 reviews were retrieved from the database, which involve 42,900 keywords, 176 countries/regions, 19,065 institutions, 147,225 authors and 4,251 journals. The gut microbiome and disease research is active and has received increasing attention. Co-cited reference analysis revealed the landmark articles in the field. The United States had the largest number of publications and close cooperation with other countries. The current research mainly focuses on gastrointestinal diseases, such as inflammatory bowel disease (IBD), ulcerative colitis (UC) and Crohn's disease (CD), while extra-intestinal diseases are also rising, such as obesity, diabetes, cardiovascular disease, Alzheimer's disease, Parkinson's disease. Omics technologies, fecal microbiota transplantation (FMT) and metabolites linked to mechanism would be more concerned in the future. Conclusion The gut microbiome and disease has been a booming field of research, and the trend is expected to continue. Overall, this research field shows a multitude of challenges and great opportunities.
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58
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Xin JY, Wang J, Ding QQ, Chen W, Xu XK, Wei XT, Lv YH, Wei YP, Feng Y, Zu XP. Potential role of gut microbiota and its metabolites in radiation-induced intestinal damage. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 248:114341. [PMID: 36442401 DOI: 10.1016/j.ecoenv.2022.114341] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/13/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Radiation-induced intestinal damage (RIID) is a serious disease with limited effective treatment. Nuclear explosion, nuclear release, nuclear application and especially radiation therapy are all highly likely to cause radioactive intestinal damage. The intestinal microecology is an organic whole with a symbiotic relationship formed by the interaction between a relatively stable microbial community living in the intestinal tract and the host. Imbalance and disorders of intestinal microecology are related to the occurrence and development of multiple systemic diseases, especially intestinal diseases. Increasing evidence indicates that the gut microbiota and its metabolites play an important role in the pathogenesis and prevention of RIID. Radiation leads to gut microbiota imbalance, including a decrease in the number of beneficial bacteria and an increase in the number of harmful bacteria that cause RIID. In this review, we describe the pathological mechanisms of RIID, the changes in intestinal microbiota, the metabolites induced by radiation, and their mechanism in RIID. Finally, the mechanisms of various methods for regulating the microbiota in the treatment of RIID are summarized.
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Affiliation(s)
- Jia-Yun Xin
- School of Pharmacy, Naval Medical University, Shanghai 200433, China; School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Jie Wang
- School of Pharmacy, Naval Medical University, Shanghai 200433, China; School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Qian-Qian Ding
- School of Pharmacy, Naval Medical University, Shanghai 200433, China; School of Pharmacy, Anhui University of Traditional Chinese Medicine, Hefei 230012, China
| | - Wei Chen
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Xi-Ke Xu
- School of Pharmacy, Naval Medical University, Shanghai 200433, China
| | - Xin-Tong Wei
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yan-Hui Lv
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yan-Ping Wei
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Yu Feng
- School of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan 250355, China.
| | - Xian-Peng Zu
- School of Pharmacy, Naval Medical University, Shanghai 200433, China.
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Loganathan T, Priya Doss C G. The influence of machine learning technologies in gut microbiome research and cancer studies - A review. Life Sci 2022; 311:121118. [DOI: 10.1016/j.lfs.2022.121118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/19/2022] [Accepted: 10/19/2022] [Indexed: 11/18/2022]
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ACSL4 is essential for radiation-induced intestinal injury by initiating ferroptosis. Cell Death Discov 2022; 8:332. [PMID: 35869042 PMCID: PMC9307849 DOI: 10.1038/s41420-022-01127-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/07/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Lipid peroxidation-induced ferroptosis is a newly recognized type of programmed cell death. With the method of RNA sequencing, we found that irradiation (IR) markedly increased the expression of ferroptosis promotive genes, whereas reduced the expression of ferroptosis suppressive genes in murine intestine tissues, when compared with those of liver and lung tissues. By using ferroptosis inducer RSL-3 and inhibitor liproxstatin-1, we found that ferroptosis is essential for IR-induced intestinal injury. Acyl-CoA Synthetase Long-Chain Family Member 4 (ACSL4) is an important component for ferroptosis execution, and we found that ACSL4 expression was significantly upregulated in irradiated intestine tissues, but not in liver or lung tissues. Antibacterial and antifungal regents reduced the expression of ASCL4 and protected against tissue injury in irradiated intestine tissues. Further studies showed that troglitazone, a ACSL4 inhibitor, succeeded to suppresses intestine lipid peroxidation and tissue damage after IR.
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61
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Wang JS, Liu JC. Intestinal microbiota in the treatment of metabolically associated fatty liver disease. World J Clin Cases 2022; 10:11240-11251. [PMID: 36387806 PMCID: PMC9649557 DOI: 10.12998/wjcc.v10.i31.11240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/07/2022] [Accepted: 09/27/2022] [Indexed: 02/05/2023] Open
Abstract
Metabolically associated fatty liver disease (MAFLD) is a common cause of chronic liver disease, the hepatic manifestation of metabolic syndrome. Despite the increasing incidence of MAFLD, no effective treatment is available. Recent research indicates a link between the intestinal microbiota and liver diseases such as MAFLD. The composition and characteristics of the intestinal microbiota and therapeutic perspectives of MAFLD are reviewed in the current study. An imbalance in the intestinal microbiota increases intestinal permeability and exposure of the liver to adipokines. Furthermore, we focused on reviewing the latest "gut-liver axis" targeted therapy.
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Affiliation(s)
- Ji-Shuai Wang
- Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
| | - Jin-Chun Liu
- Department of Gastroenterology, The First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi Province, China
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62
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Bartolini I, Nannini G, Risaliti M, Matarazzo F, Moraldi L, Ringressi MN, Taddei A, Amedei A. Impact of microbiota-immunity axis in pancreatic cancer management. World J Gastroenterol 2022; 28:4527-4539. [PMID: 36157926 PMCID: PMC9476869 DOI: 10.3748/wjg.v28.i32.4527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/28/2022] [Accepted: 07/27/2022] [Indexed: 02/06/2023] Open
Abstract
The microbiota impact on human diseases is well-known, and a growing body of literature is providing evidence about the complex interplay between microbiota-immune system-human physiology/pathology, including cancers. Together with the defined risk factors (e.g., smoke habits, diet, diabetes, and obesity), the oral, gut, biliary, and intrapancreatic microbiota contribute to pancreatic cancer development through different pathways including the interaction with the immune system. Unfortunately, a great majority of the pancreatic cancer patients received a diagnosis in advanced stages not amenable to be radically treated and potentially cured. Given the poor pancreatic cancer prognosis, complete knowledge of these complicated relationships could help researchers better understand the disease pathogenesis and thus provide early potential non-invasive biomarkers, new therapeutic targets, and tools for risk stratification that might result in greater therapeutic possibilities and eventually in a better and longer patient survival.
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Affiliation(s)
- Ilenia Bartolini
- Department of Experimental and Clinical Medicine, HPB Surgery Unit, Azienda Ospedaliero-Universitaria Careggi, Florence 50134, Italy
| | - Giulia Nannini
- Department of Experimental and Clinical Medicine, SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera-Universitaria Careggi, Florence 50134, Italy
| | - Matteo Risaliti
- Department of Experimental and Clinical Medicine, HPB Surgery Unit, Azienda Ospedaliero-Universitaria Careggi, Florence 50134, Italy
| | - Francesco Matarazzo
- Department of Experimental and Clinical Medicine, HPB Surgery Unit, Azienda Ospedaliero-Universitaria Careggi, Florence 50134, Italy
| | - Luca Moraldi
- Division of Oncologic Surgery, Department of Oncology, Careggi University Hospital, Firenze 50134, Italy
| | - Maria Novella Ringressi
- Department of Experimental and Clinical Medicine, HPB Surgery Unit, Azienda Ospedaliero-Universitaria Careggi, Florence 50134, Italy
| | - Antonio Taddei
- Department of Experimental and Clinical Medicine, HPB Surgery Unit, Azienda Ospedaliero-Universitaria Careggi, Florence 50134, Italy
| | - Amedeo Amedei
- Department of Experimental and Clinical Medicine, SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera-Universitaria Careggi, Florence 50134, Italy
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Martínez-López YE, Esquivel-Hernández DA, Sánchez-Castañeda JP, Neri-Rosario D, Guardado-Mendoza R, Resendis-Antonio O. Type 2 diabetes, gut microbiome, and systems biology: A novel perspective for a new era. Gut Microbes 2022; 14:2111952. [PMID: 36004400 PMCID: PMC9423831 DOI: 10.1080/19490976.2022.2111952] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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
The association between the physio-pathological variables of type 2 diabetes (T2D) and gut microbiota composition suggests a new avenue to track the disease and improve the outcomes of pharmacological and non-pharmacological treatments. This enterprise requires new strategies to elucidate the metabolic disturbances occurring in the gut microbiome as the disease progresses. To this end, physiological knowledge and systems biology pave the way for characterizing microbiota and identifying strategies in a move toward healthy compositions. Here, we dissect the recent associations between gut microbiota and T2D. In addition, we discuss recent advances in how drugs, diet, and exercise modulate the microbiome to favor healthy stages. Finally, we present computational approaches for disentangling the metabolic activity underlying host-microbiota codependence. Altogether, we envision that the combination of physiology and computational modeling of microbiota metabolism will drive us to optimize the diagnosis and treatment of T2D patients in a personalized way.
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Affiliation(s)
- Yoscelina Estrella Martínez-López
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN). México City, México,Programa de Doctorado en Ciencias Médicas, Odontológicas y de la Salud, Universidad Nacional Autónoma de México (UNAM). Ciudad de México, México,Metabolic Research Laboratory, Department of Medicine and Nutrition. University of Guanajuato. León, Guanajuato, México
| | | | - Jean Paul Sánchez-Castañeda
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN). México City, México,Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM). Ciudad de México, México
| | - Daniel Neri-Rosario
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN). México City, México,Programa de Maestría en Ciencias Bioquímicas, Universidad Nacional Autónoma de México (UNAM). Ciudad de México, México
| | - Rodolfo Guardado-Mendoza
- Metabolic Research Laboratory, Department of Medicine and Nutrition. University of Guanajuato. León, Guanajuato, México,Research Department, Hospital Regional de Alta Especialidad del Bajío. León, Guanajuato, México,Rodolfo Guardado-Mendoza Metabolic Research Laboratory, Department of Medicine and Nutrition. University of Guanajuato. León, Guanajuato, México
| | - Osbaldo Resendis-Antonio
- Human Systems Biology Laboratory. Instituto Nacional de Medicina Genómica (INMEGEN). México City, México,Coordinación de la Investigación Científica – Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México (UNAM). Ciudad de México, México,CONTACT Osbaldo Resendis-Antonio Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (UNAM), Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610 Ciudad de México, CDMX
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64
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Feeding Our Microbiota: Stimulation of the Immune/Semiochemical System and the Potential Amelioration of Non-Communicable Diseases. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081197. [PMID: 36013376 PMCID: PMC9410320 DOI: 10.3390/life12081197] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 12/12/2022]
Abstract
Non-communicable diseases are those conditions to which causative infectious agents cannot readily be assigned. It is increasingly likely that at least some of these conditions are due to the breakdown of the previously mutualistic intestinal microbiota under the influence of a polluted, biocide-rich, environment. Following the mid-20th century African studies of Denis Burkitt, the environmental cause of conditions such as obesity has been ascribed to the absence of sufficient fibre in the modern diet, however in itself that is insufficient to explain the parallel rise of problems with both the immune system and of mental health. Conversely, Burkitt himself noted that the Maasai, a cattle herding people, remained healthy even with their relatively low intake of dietary fibre. Interestingly, however, Burkitt also emphasised that levels of non-communicable disease within a population rose as faecal weight decreased significantly, to about one third of the levels found in healthy populations. Accordingly, a more cogent explanation for all the available facts is that the fully functioning, adequately diverse microbiome, communicating through what has been termed the microbiota–gut–brain axis, helps to control the passage of food through the digestive tract to provide itself with the nutrition it needs. The method of communication is via the production of semiochemicals, interkingdom signalling molecules, potentially including dopamine. In turn, the microbiome aids the immune system of both adult and, most importantly, the neonate. In this article we consider the role of probiotics and prebiotics, including fermented foods and dietary fibre, in the stimulation of the immune system and of semiochemical production in the gut lumen. Finally, we reprise our suggestion of an ingestible sensor, calibrated to the detection of such semiochemicals, to assess both the effectiveness of individual microbiomes and methods of amelioration of the associated non-communicable diseases.
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Yang L, Hung LY, Zhu Y, Ding S, Margolis KG, Leong KW. Material Engineering in Gut Microbiome and Human Health. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9804014. [PMID: 35958108 PMCID: PMC9343081 DOI: 10.34133/2022/9804014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/10/2022] [Indexed: 12/11/2022]
Abstract
Tremendous progress has been made in the past decade regarding our understanding of the gut microbiome's role in human health. Currently, however, a comprehensive and focused review marrying the two distinct fields of gut microbiome and material research is lacking. To bridge the gap, the current paper discusses critical aspects of the rapidly emerging research topic of "material engineering in the gut microbiome and human health." By engaging scientists with diverse backgrounds in biomaterials, gut-microbiome axis, neuroscience, synthetic biology, tissue engineering, and biosensing in a dialogue, our goal is to accelerate the development of research tools for gut microbiome research and the development of therapeutics that target the gut microbiome. For this purpose, state-of-the-art knowledge is presented here on biomaterial technologies that facilitate the study, analysis, and manipulation of the gut microbiome, including intestinal organoids, gut-on-chip models, hydrogels for spatial mapping of gut microbiome compositions, microbiome biosensors, and oral bacteria delivery systems. In addition, a discussion is provided regarding the microbiome-gut-brain axis and the critical roles that biomaterials can play to investigate and regulate the axis. Lastly, perspectives are provided regarding future directions on how to develop and use novel biomaterials in gut microbiome research, as well as essential regulatory rules in clinical translation. In this way, we hope to inspire research into future biomaterial technologies to advance gut microbiome research and gut microbiome-based theragnostics.
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Affiliation(s)
- Letao Yang
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Lin Y. Hung
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Yuefei Zhu
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Suwan Ding
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Kara G. Margolis
- Department of Pediatrics, Columbia University, New York, New York, USA
| | - Kam W. Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
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66
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Lobanov V, Gobet A, Joyce A. Ecosystem-specific microbiota and microbiome databases in the era of big data. ENVIRONMENTAL MICROBIOME 2022; 17:37. [PMID: 35842686 PMCID: PMC9287977 DOI: 10.1186/s40793-022-00433-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 06/29/2022] [Indexed: 05/05/2023]
Abstract
The rapid development of sequencing methods over the past decades has accelerated both the potential scope and depth of microbiota and microbiome studies. Recent developments in the field have been marked by an expansion away from purely categorical studies towards a greater investigation of community functionality. As in-depth genomic and environmental coverage is often distributed unequally across major taxa and ecosystems, it can be difficult to identify or substantiate relationships within microbial communities. Generic databases containing datasets from diverse ecosystems have opened a new era of data accessibility despite costs in terms of data quality and heterogeneity. This challenge is readily embodied in the integration of meta-omics data alongside habitat-specific standards which help contextualise datasets both in terms of sample processing and background within the ecosystem. A special case of large genomic repositories, ecosystem-specific databases (ES-DB's), have emerged to consolidate and better standardise sample processing and analysis protocols around individual ecosystems under study, allowing independent studies to produce comparable datasets. Here, we provide a comprehensive review of this emerging tool for microbial community analysis in relation to current trends in the field. We focus on the factors leading to the formation of ES-DB's, their comparison to traditional microbial databases, the potential for ES-DB integration with meta-omics platforms, as well as inherent limitations in the applicability of ES-DB's.
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Affiliation(s)
- Victor Lobanov
- Department of Marine Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden
| | | | - Alyssa Joyce
- Department of Marine Sciences, University of Gothenburg, Box 461, 405 30, Gothenburg, Sweden.
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67
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Kumari R, Yadav Y, Misra R, Das U, Das Adhikari U, Malakar P, Dubey GP. Emerging frontiers of antibiotics use and their impacts on the human gut microbiome. Microbiol Res 2022; 263:127127. [PMID: 35914416 DOI: 10.1016/j.micres.2022.127127] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/17/2022] [Accepted: 07/11/2022] [Indexed: 02/07/2023]
Abstract
Antibiotics, the primary drugs used to cure bacterial diseases, are increasingly becoming ineffective due to the emergence of multiple drug resistance (MDR) leading to recurrence of previously sensitive pathogens. Human gut microbiome (GM), known to play an important role in various physiological processes, consists of pool of diverse microbes. Indiscriminate use of antibiotics during the life span of an individual may lead to development of resistant microbes e.g. Vibrio, Acinetobacter, Escherichia, Klebsiella, Clostridia, etc. in the human GM. Transmission of antibiotic resistant genes (ARGs) between pathogenic and commensal bacteria occurs more frequently in microbiome communities wherein bacteria communicate and exchange cellular constituents both among themselves and with the host. Additionally, co-factors like 'early vs. late' exposure, type of antibiotics and duration of treatment modulate the adverse effects of antibiotics on GM maturation. Furthermore, factors like mode of birth, ethnicity, malnutrition, demography, diet, lifestyle, etc., which influence GM composition, can also indirectly alter the host response to antibiotics. Currently, advanced 'omics' and culturomics approaches are revealing novel avenues to study the interplay between antibiotics and the microbiome and to identify resistant genes in these bacterial communities. Here, we discuss the recent developments that have given insights into the effects of antibiotics on the homeostatic balance of the gut microbiome and thus on human health.
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Affiliation(s)
- Rekha Kumari
- Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
| | - Yasha Yadav
- Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India
| | - Richa Misra
- Department of Zoology, Sri Venkateswara College, University of Delhi, Delhi 1100021, India
| | - Utpal Das
- Department of Neurosciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Upasana Das Adhikari
- The Ragon Institute of MGH, MIT and Harvard, 400 Technology Square Cambridge, MA 02139, USA
| | - Pushkar Malakar
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gyanendra P Dubey
- Molecular Microbial Pathogenesis Unit, Institut Pasteur, 28 rue du Docteur Roux, 75724 Cedex 15 Paris, France.
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Borreliella burgdorferi Antimicrobial-Tolerant Persistence in Lyme Disease and Posttreatment Lyme Disease Syndromes. mBio 2022; 13:e0344021. [PMID: 35467428 PMCID: PMC9239140 DOI: 10.1128/mbio.03440-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The annual incidence of Lyme disease, caused by tick-transmitted Borreliella burgdorferi, is estimated to be at least 476,000 cases in the United States and many more worldwide. Ten to 20% of antimicrobial-treated Lyme disease patients display posttreatment Lyme disease syndrome (PTLDS), a clinical complication whose etiology and pathogenesis remain uncertain. Autoimmunity, cross-reactivity, molecular mimicry, coinfections, and borrelial tolerance to antimicrobials/persistence have been hypothesized and studied as potential causes of PTLDS. Studies of borrelial tolerance/persistence in vitro in response to antimicrobials and experimental studies in mice and nonhuman primates, taken together with clinical reports, have revealed that B. burgdorferi becomes tolerant to antimicrobials and may sometimes persist in animals and humans after the currently recommended antimicrobial treatment. Moreover, B. burgdorferi is pleomorphic and can generate viable-but-nonculturable bacteria, states also involved in antimicrobial tolerance. The multiple regulatory pathways and structural genes involved in mediating this tolerance to antimicrobials and environmental stressors by persistence might include the stringent (rel and dksA) and host adaptation (rpoS) responses, sugar metabolism (glpD), and polypeptide transporters (opp). Application of this recently reported knowledge to clinical studies can be expected to clarify the potential role of bacterial antibacterial tolerance/persistence in Lyme disease and PTLDS.
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Microbiome–Gut Dissociation in the Neonate: Obesity and Coeliac Disease as Examples of Microbiome Function Deficiency Disorder. GASTROINTESTINAL DISORDERS 2022. [DOI: 10.3390/gidisord4030012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The purpose of this article is to provide a direction for translational research based on an analysis of the nature of complex, immune-related conditions such as obesity and coeliac disease. In essence, it seems that the prevalence of these non-communicable diseases is related to the degradation of the microbiome during the industrialisation of society, and that their nature can be used to infer the functions of the “pre-industrial” microbiome. Based on this analysis, the key point is the necessity for the fully functioning microbiome, acting alongside the parental genetic inheritance of the child, to be in place immediately after birth. In our view, this is achieved by the seemingly accidental process of maternal microbial inheritance during normal birth. Note, however, that this is not possible if the microbiome of the mother is itself degraded following previous problems. Under these conditions the health of a child may be affected from the moment of birth, although, with the exception of atopic diseases, such as eczema and food allergy, the consequences may not become apparent until late childhood or as an adult. In this way, this microbiome function deficiency hypothesis incorporates the epidemiological observations of David Strachan and David Barker in that their onset can be traced to early childhood. Coeliac disease has been chosen as an illustrative example of a multifactorial disorder due to the fact that, in addition to a series of immune system manifestations and a potential problem with food absorption, there is also a significant psychological component. Finally, it is worth noting that an ingestible sensor calibrated to the detection of interkingdom communication molecules (semiochemicals) within the intestine may offer a practical way of assessment and, perhaps, amelioration of at least some of the consequences of non-communicable disease.
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Boudar Z, Sehli S, El Janahi S, Al Idrissi N, Hamdi S, Dini N, Brim H, Amzazi S, Nejjari C, Lloyd-Puryear M, Ghazal H. Metagenomics Approaches to Investigate the Neonatal Gut Microbiome. Front Pediatr 2022; 10:886627. [PMID: 35799697 PMCID: PMC9253679 DOI: 10.3389/fped.2022.886627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/23/2022] [Indexed: 12/03/2022] Open
Abstract
Early infancy is critical for the development of an infant's gut flora. Many factors can influence microbiota development during the pre- and postnatal periods, including maternal factors, antibiotic exposure, mode of delivery, dietary patterns, and feeding type. Therefore, investigating the connection between these variables and host and microbiome interactions in neonatal development would be of great interest. As the "unculturable" era of microbiome research gives way to an intrinsically multidisciplinary field, microbiome research has reaped the advantages of technological advancements in next-generation sequencing, particularly 16S rRNA gene amplicon and shotgun sequencing, which have considerably expanded our knowledge about gut microbiota development during early life. Using omics approaches to explore the neonatal microbiome may help to better understand the link between the microbiome and newborn diseases. Herein, we summarized the metagenomics methods and tools used to advance knowledge on the neonatal microbiome origin and evolution and how the microbiome shapes early and late individuals' lives for health and disease. The way to overcome limitations in neonatal microbiome studies will be discussed.
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Affiliation(s)
- Zakia Boudar
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Sofia Sehli
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Sara El Janahi
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
| | - Najib Al Idrissi
- Department of Surgery, Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Salsabil Hamdi
- Laboratory of Genomics and Bioinformatics, School of Pharmacy, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Nouzha Dini
- Mother and Child Department, Cheikh Khalifa International University Hospital, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Hassan Brim
- Department of Pathology, Howard University, Washington, DC, United States
| | - Saaïd Amzazi
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Chakib Nejjari
- Department of Epidemiology and Biostatistics, International School of Public Health, Mohammed VI University of Health Sciences, Casablanca, Morocco
- Department of Epidemiology and Public Health, Faculty of Medicine, University Sidi Mohammed Ben Abdellah, Fez, Morocco
| | | | - Hassan Ghazal
- Department of Fundamental Sciences, School of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco
- National Center for Scientific and Technical Research, Rabat, Morocco
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Ferrocino I, Rantsiou K, Cocolin L. Microbiome and -omics application in food industry. Int J Food Microbiol 2022; 377:109781. [DOI: 10.1016/j.ijfoodmicro.2022.109781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/31/2022] [Accepted: 06/03/2022] [Indexed: 11/30/2022]
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Cerk K, Aguilera‐Gómez M. Microbiota analysis for risk assessment: evaluation of hazardous dietary substances and its potential role on the gut microbiome variability and dysbiosis. EFSA J 2022; 20:e200404. [PMID: 35634548 PMCID: PMC9131584 DOI: 10.2903/j.efsa.2022.e200404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The expansion of fields related to probiotics, microbiome‐targeted interventions and an evolving landscape for implementation across policy, industry and end users, signifies an era of important clinical translational changes. Characteristics and perception of traditional probiotics stemmed from the historical long‐term use of fermented products. Although the distinction between probiotic microorganisms and fermentation‐associated microbes is important, it is often confused as not all fermented foods are probiotic supplements. Current innovation in area of biotechnology and bioinformatics is emerging outside of the classical definitions and new probiotics will emerge from novel sources, challenging scientific as well as regulatory instructions. At the same time, the search for individual and group microbiome signatures – biomarkers in order to predict disease incidence, progression and response to treatment is a key area of microbiological and multidisciplinary research, enabled by efficient and powerful processing of large data sets. However, the regulation of marketed beneficial microbes and probiotics differs among countries and the basic level of classification, which depend on probiotic classification is not globally harmonised. At the same time, the regulation is very demanding to evaluate the safety of products on the market, so that only those products with scientific evidence benefits can obtain positive recognition in ways of health claims. Collaborative experimental and theoretical approaches and case studies have assisted the progress in this crosscutting area of research. There is a requirement to clearly specify criteria and provide details about ways and approaches of achieving those criteria with the intention that manufacturers can benefit from a transparent way of communicating product quality to end users.
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Doualeh M, Payne M, Litton E, Raby E, Currie A. Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis. Int J Mol Sci 2022; 23:ijms23094484. [PMID: 35562877 PMCID: PMC9104822 DOI: 10.3390/ijms23094484] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 12/19/2022] Open
Abstract
Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host–pathogen interplay is well described, less is known about the pathogen’s role, including pathogen–pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.
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Affiliation(s)
- Mariam Doualeh
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
| | - Matthew Payne
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Division of Obstetrics and Gynaecology, University of Western Australia, Perth, WA 6008, Australia
| | - Edward Litton
- Intensive Care Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Intensive Care Unit, St. John of God Hospital, Subiaco, WA 6009, Australia
| | - Edward Raby
- State Burns Unit, Fiona Stanley Hospital, Murdoch, WA 6150, Australia;
- Microbiology Department, Path West Laboratory Medicine, Murdoch, WA 6150, Australia
| | - Andrew Currie
- Centre for Molecular Medicine & Innovative Therapeutics, Murdoch University, Murdoch, WA 6150, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
- Women and Infants Research Foundation, Perth, WA 6008, Australia;
- Correspondence: ; Tel.: +61-(08)-9360-7426
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Abstract
Newer 'omics approaches, such as metatranscriptomics and metabolomics, allow functional assessments of the interaction(s) between the gut microbiome and the human host. However, in order to generate meaningful data with these approaches, the method of sample collection is critical. Prior studies have relied on expensive and invasive means toward sample acquisition, such as intestinal biopsy, while other studies have relied on easier methods of collection, such as fecal samples that do not necessarily represent those microbes in contact with the host. In this pilot study, we attempt to characterize a novel, minimally invasive method toward sampling the human microbiome using mucosal cytology brush sampling compared to intestinal gut biopsy samples on 5 healthy participants undergoing routine screening colonoscopy. We compared metatranscriptomic analyses between the two collection methods and identified increased taxonomic evenness and beta diversity in the cytology brush samples and similar community transcriptional profiles between the two methods. Metabolomics assessment demonstrated striking differences between the two methods, implying a difference in bacterial-derived versus human-absorbed metabolites. Put together, this study supports the use of microbiome sampling with cytology brushes, but caution must be exercised when performing metabolomics assessment, as this represents differential metabolite production but not absorption by the host. IMPORTANCE In order to generate meaningful metabolomic and microbiome data, the method of sample collection is critical. This study utilizes and compares two methods for intestinal tissue collection for evaluation of metabolites and microbiomes, finding that using a brush to sample the microbiome provides valuable data. However, for metabolomics assessment, biopsy samples may still be required.
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Mirza AI, Zhu F, Knox N, Forbes JD, Van Domselaar G, Bernstein CN, Graham M, Marrie RA, Hart J, Yeh EA, Arnold DL, Bar-Or A, O'Mahony J, Zhao Y, Hsiao W, Banwell B, Waubant E, Tremlett H. Metagenomic Analysis of the Pediatric-Onset Multiple Sclerosis Gut Microbiome. Neurology 2022; 98:e1050-e1063. [PMID: 34937787 PMCID: PMC8967388 DOI: 10.1212/wnl.0000000000013245] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 12/13/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Little is known of the functional potential of the gut microbiome in pediatric-onset multiple sclerosis (MS). We performed metagenomic analyses using stool samples from individuals with pediatric-onset MS and unaffected controls. METHODS Persons ≤21 years old enrolled in the Canadian Pediatric Demyelinating Disease Network providing a stool sample were eligible. Twenty patients with MS (McDonald criteria) with symptom onset <18 years were matched to 20 controls by sex, age (±3 years), stool consistency, and race. Microbial taxonomy and functional potentials were estimated from stool sample-derived metagenomic reads and compared by disease status (MS vs controls) and disease-modifying drug (DMD) exposure using alpha diversity, relative abundance, and prevalence using Wilcoxon rank sum, ALDEx2, and Fisher exact tests, respectively. RESULTS Individuals with MS were aged 13.6 years (mean) at symptom onset and 8 were DMD-naive. Mean ages at stool sample were 16.1 and 15.4 years for MS and control participants, respectively; 80% were girls. Alpha diversity of enzymes and proteins did not differ by disease or DMD status (p > 0.20), but metabolic pathways, gene annotations, and microbial taxonomy did. Individuals with MS (vs controls) exhibited higher methanogenesis prevalence (odds ratio 10, p = 0.044) and Methanobrevibacter abundance (log2 fold change [LFC] 1.7, p = 0.0014), but lower homolactic fermentation abundance (LFC -0.48, p = 0.039). Differences by DMD status included lower phosphate butyryl transferase for DMD-naive vs exposed patients with MS (LFC -1.0, p = 0.033). DISCUSSION The gut microbiome's functional potential and taxonomy differed between individuals with pediatric-onset MS vs controls, including higher prevalence of a methane-producing pathway from Archaea and depletion of the lactate fermentation pathway. DMD exposure was associated with butyrate-producing enzyme enrichment. Together these findings indicate that the gut microbiome of individuals with MS may have a disturbed functional potential.
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Affiliation(s)
- Ali I Mirza
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Feng Zhu
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Natalie Knox
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Jessica D Forbes
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Gary Van Domselaar
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Charles N Bernstein
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Morag Graham
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Ruth Ann Marrie
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Janace Hart
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - E Ann Yeh
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Douglas L Arnold
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Amit Bar-Or
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Julia O'Mahony
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Yinshan Zhao
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - William Hsiao
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Brenda Banwell
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Emmanuelle Waubant
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA
| | - Helen Tremlett
- From the Department of Medicine (Neurology) (A.I.M., F.Z., Y.Z., H.T.), The University of British Columbia, Vancouver; National Microbiology Laboratory (N.K., G.V.D., M.G.), Public Health Agency of Canada; Department of Medical Microbiology and Infectious Diseases (N.K., G.V.D., M.G.), Department of Internal Medicine, Max Rady College of Medicine, Rady Faculty of Health Sciences (C.N.B., R.A.M.), and Inflammatory Bowel Disease Clinical and Research Centre (C.N.B.), University of Manitoba, Winnipeg; Roy Romanow Provincial Laboratory (J.D.F.), Regina; Department of Pathology and Laboratory Medicine (J.D.F.), College of Medicine, University of Saskatchewan, Saskatoon, Canada; Department of Neurology (J.H., E.W.), University of California San Francisco; Department of Pediatrics (Neurology) (E.A.Y., J.O.), The Hospital for Sick Children, Toronto; Department of Neurology and Neurosurgery (D.L.A.), Montreal Neurological Institute, McGill University, Montreal, Canada; Centre for Neuroinflammation and Experimental Therapeutics and Department of Neurology (A.B.-O.), University of Pennsylvania Perelman School of Medicine, Philadelphia; Faculty of Health Sciences (W.H.), Simon Fraser University, Burnaby, Canada; and The Children's Hospital of Philadelphia (B.B.), PA.
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Zhang X, Walker K, Mayne J, Li L, Ning Z, Stintzi A, Figeys D. Evaluating live microbiota biobanking using an ex vivo microbiome assay and metaproteomics. Gut Microbes 2022; 14:2035658. [PMID: 35130123 PMCID: PMC8824213 DOI: 10.1080/19490976.2022.2035658] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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
Biobanking of live microbiota is becoming indispensable for mechanistic and clinical investigations of drug-microbiome interactions and fecal microbiota transplantation. However, there is a lack of methods to rapidly and systematically evaluate whether the biobanked microbiota maintains their cultivability and functional activity. In this study, we use a rapid ex vivo microbiome assay and metaproteomics to evaluate the cultivability and the functional responses of biobanked microbiota to treatment with a prebiotic (fructo-oligosaccharide, FOS). Our results indicate that the microbiota cultivability and their functional responses to FOS treatment were well maintained by freezing in a deoxygenated glycerol buffer at -80°C for 12 months. We also demonstrate that the fecal microbiota is functionally stable for 48 hours on ice in a deoxygenated glycerol buffer, allowing off-site fecal sample collection and shipping to laboratory for live microbiota biobanking. This study provides a method for rapid evaluation of the cultivability of biobanked live microbiota. Our results show minimal detrimental influences of long-term freezing in deoxygenated glycerol buffer on the cultivability of fecal microbiota.
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Affiliation(s)
- Xu Zhang
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Krystal Walker
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Janice Mayne
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Leyuan Li
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Zhibin Ning
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Alain Stintzi
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Daniel Figeys
- School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada,CONTACT Daniel Figeys School of Pharmaceutical Sciences, Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Room 4510D, 451 Smyth Road, Ottawa, ONK1H 8M5, Canada
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77
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Smith D, Palacios-Pérez M, Jheeta S. The Enclosed Intestinal Microbiome: Semiochemical Signals from the Precambrian and Their Disruption by Heavy Metal Pollution. Life (Basel) 2022; 12:287. [PMID: 35207574 PMCID: PMC8879143 DOI: 10.3390/life12020287] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 12/12/2022] Open
Abstract
It is increasingly likely that many non-communicable diseases of humans and associated animals are due to the degradation of their intestinal microbiomes, a situation often referred to as dysbiosis. An analysis of the resultant diseases offers an opportunity to probe the function of these microbial partners of multicellular animals. In our view, it now seems likely that vertebrate animals and their microbiomes have coevolved throughout the Ediacaran-Cambrian transition and beyond, operating by semiochemical messaging between the multicellular host and its microbial community guest. A consideration of the overall role of the mutualistic intestinal microbiome as an enclosed bioreactor throws up a variety of challenging concepts. In particular: the significance of the microbiome with respect to the immune system suggests that microeukaryotes could act as microbial sentinel cells; the ubiquity of bacteriophage viruses implies the rapid turnover of microbial composition by a viral-shunt mechanism; and high microbial diversity is needed to ensure that horizontal gene transfer allows valuable genetic functions to be expressed. We have previously postulated that microbes of sufficient diversity must be transferred from mother to infant by seemingly accidental contamination during the process of natural birth. We termed this maternal microbial inheritance and suggested that it operates alongside parental genetic inheritance to modify gene expression. In this way, the adjustment of the neonate immune system by the microbiome may represent one of the ways in which the genome of a vertebrate animal interacts with its microbial environment. The absence of such critical functions in the neonate may help to explain the observation of persistent immune-system problems in affected adults. Equally, granted that the survival of the guest microbiome depends on the viability of its host, one function of microbiome-generated semiochemicals could be to facilitate the movement of food through the digestive tract, effectively partitioning nutrition between host and guest. In the event of famine, downregulation of microbial growth and therefore of semiochemical production would allow all available food to be consumed by the host. Although it is often thought that non-communicable diseases, such as type 2 diabetes, are caused by consumption of food containing insufficient dietary fibre, our hypothesis suggests that poor-quality food is not the prime cause but that the tendency for disease follows the degradation of the intestinal microbiome, when fat build-up occurs because the relevant semiochemicals can no longer be produced. It is the purpose of this paper to highlight the possibility that the origins of the microbiome lie in the Precambrian and that the disconnection of body and microbiome gives rise to non-communicable disease through the loss of semiochemical signalling. We further surmise that this disconnect has been largely brought about by heavy metal poisoning, potentially illuminating a facet of the exposome, the sum total of environmental insults that influence the expression of the genetic inheritance of an animal.
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Affiliation(s)
- David Smith
- Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds LS7 3RB, UK
| | - Miryam Palacios-Pérez
- Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds LS7 3RB, UK
- Theoretical Biology Group, Institute of Biomedical Research, National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Sohan Jheeta
- Network of Researchers on the Chemical Evolution of Life (NoRCEL), Leeds LS7 3RB, UK
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78
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Bhat SA, Kaur R, Chauhan A, Pal A. The microbiome and precision oncology: an emerging paradigm in anticancer therapy. Crit Rev Microbiol 2022; 48:770-783. [PMID: 35164642 DOI: 10.1080/1040841x.2022.2035313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the host-microbiome interactions has emerged as an essential factor in improving human health and disease. Recent advances in understanding the intimate relationship of microbes with the host have uncovered various previously unknown underlying causes of disease development, progression, and treatment failure. The dynamic behaviour of the microbiome confers the heterogeneity in treatment response by modulating the immune response and inflammation in various diseases, including cancer. The growing insights into the microbial modulation of cancer through immunoregulation, xenometabolism, and increase in toxicity open a new era of personalised medicine. In the current review, we discuss the essential roles played by the microbiome in modulating the efficacy and toxicity of anticancer therapies (immunotherapy, chemotherapy, and radiotherapy). We also outline the current state of personalised medicine in the context of cancer and microbiome modulation. The knowledge about the role of cancer-microbiome communication will lead to designing other precise microbial modulation strategies for cancer treatment through enhanced efficacy and decreased toxicity.
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Affiliation(s)
- Shabir Ahmad Bhat
- Department of Biochemistry, PostGraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rajandeep Kaur
- Department of Biochemistry, PostGraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anshika Chauhan
- Department of Biochemistry, PostGraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arnab Pal
- Department of Biochemistry, PostGraduate Institute of Medical Education and Research, Chandigarh, India
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79
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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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80
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Mills RH, Dulai PS, Vázquez-Baeza Y, Sauceda C, Daniel N, Gerner RR, Batachari LE, Malfavon M, Zhu Q, Weldon K, Humphrey G, Carrillo-Terrazas M, Goldasich LD, Bryant M, Raffatellu M, Quinn RA, Gewirtz AT, Chassaing B, Chu H, Sandborn WJ, Dorrestein PC, Knight R, Gonzalez DJ. Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity. Nat Microbiol 2022; 7:262-276. [PMID: 35087228 PMCID: PMC8852248 DOI: 10.1038/s41564-021-01050-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/15/2021] [Indexed: 12/19/2022]
Abstract
Ulcerative colitis (UC) is driven by disruptions in host-microbiota homoeostasis, but current treatments exclusively target host inflammatory pathways. To understand how host-microbiota interactions become disrupted in UC, we collected and analysed six faecal- or serum-based omic datasets (metaproteomic, metabolomic, metagenomic, metapeptidomic and amplicon sequencing profiles of faecal samples and proteomic profiles of serum samples) from 40 UC patients at a single inflammatory bowel disease centre, as well as various clinical, endoscopic and histologic measures of disease activity. A validation cohort of 210 samples (73 UC, 117 Crohn's disease, 20 healthy controls) was collected and analysed separately and independently. Data integration across both cohorts showed that a subset of the clinically active UC patients had an overabundance of proteases that originated from the bacterium Bacteroides vulgatus. To test whether B. vulgatus proteases contribute to UC disease activity, we first profiled B. vulgatus proteases found in patients and bacterial cultures. Use of a broad-spectrum protease inhibitor improved B. vulgatus-induced barrier dysfunction in vitro, and prevented colitis in B. vulgatus monocolonized, IL10-deficient mice. Furthermore, transplantation of faeces from UC patients with a high abundance of B. vulgatus proteases into germfree mice induced colitis dependent on protease activity. These results, stemming from a multi-omics approach, improve understanding of functional microbiota alterations that drive UC and provide a resource for identifying other pathways that could be inhibited as a strategy to treat this disease.
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Affiliation(s)
- Robert H Mills
- Department of Pharmacology, University of California, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA
| | - Parambir S Dulai
- Division of Gastroenterology, University of California, San Diego, CA, USA
| | - Yoshiki Vázquez-Baeza
- Department of Pediatrics, University of California, San Diego, CA, USA.,Department of Computer Science and Engineering, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Consuelo Sauceda
- Department of Pharmacology, University of California, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Noëmie Daniel
- INSERM U1016, team Mucosal microbiota in chronic inflammatory diseases, CNRS UMR 8104, Université de Paris, Paris, France
| | - Romana R Gerner
- Department of Pediatrics, University of California, San Diego, CA, USA.,Division of Host-Microbe Systems and Therapeutics, University of California, San Diego, CA, USA
| | | | - Mario Malfavon
- Department of Pharmacology, University of California, San Diego, CA, USA
| | - Qiyun Zhu
- Department of Pediatrics, University of California, San Diego, CA, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Kelly Weldon
- Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Marvic Carrillo-Terrazas
- Department of Pharmacology, University of California, San Diego, CA, USA.,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pathology, University of California, San Diego, CA, USA
| | | | - MacKenzie Bryant
- Department of Pediatrics, University of California, San Diego, CA, USA
| | - Manuela Raffatellu
- Center for Microbiome Innovation, University of California, San Diego, CA, USA.,Division of Host-Microbe Systems and Therapeutics, University of California, San Diego, CA, USA
| | - Robert A Quinn
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - Andrew T Gewirtz
- Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Benoit Chassaing
- INSERM U1016, team Mucosal microbiota in chronic inflammatory diseases, CNRS UMR 8104, Université de Paris, Paris, France
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, CA, USA
| | - William J Sandborn
- Division of Gastroenterology, University of California, San Diego, CA, USA
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, CA, USA. .,Department of Computer Science and Engineering, University of California, San Diego, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, CA, USA.
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, CA, USA. .,Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA. .,Center for Microbiome Innovation, University of California, San Diego, CA, USA.
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81
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Kim J, Lee HK. Potential Role of the Gut Microbiome In Colorectal Cancer Progression. Front Immunol 2022; 12:807648. [PMID: 35069592 PMCID: PMC8777015 DOI: 10.3389/fimmu.2021.807648] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022] Open
Abstract
An increasing number of studies have revealed that the progression of colorectal cancer (CRC) is related to gut microbiome composition. Under normal conditions, the gut microbiome acts as a barrier to other pathogens or infections in the intestine and modulates inflammation by affecting the host immune system. These gut microbiota are not only related to the intestinal inflammation associated with tumorigenesis but also modulation of the anti-cancer immune response. Thus, they are associated with tumor progression and anti-cancer treatment efficacy. Studies have shown that the gut microbiota can be used as biomarkers to predict the effect of immunotherapy and improve the efficacy of immunotherapy in treating CRC through modulation. In this review, we discuss the role of the gut microbiome as revealed by recent studies of the growth and progression of CRC along with its synergistic effect with anti-cancer treatment modalities.
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Affiliation(s)
- Jaeho Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Heung Kyu Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
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82
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Salachan PV, Sørensen KD. Dysbiotic microbes and how to find them: a review of microbiome profiling in prostate cancer. J Exp Clin Cancer Res 2022; 41:31. [PMID: 35065652 PMCID: PMC8783429 DOI: 10.1186/s13046-021-02196-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022] Open
Abstract
The role of the microbiota in human health and disease is well established, including its effects on several cancer types. However, the role of microbial dysbiosis in prostate cancer development, progression, and response to treatment is less well understood. This knowledge gap could perhaps be implicated in the lack of better risk stratification and prognostic tools that incorporate risk factors such as bacterial infections and inflammatory signatures. With over a decade’s research investigating associations between microbiome and prostate carcinogenesis, we are ever closer to finding the crucial biological link between the two. Yet, definitive answers remain elusive, calling for continued research into this field. In this review, we outline the three frequently used NGS based analysis methodologies that are used for microbiome profiling, thereby serving as a quick guide for future microbiome research. We next provide a detailed overview of the current knowledge of the role of the human microbiome in prostate cancer development, progression, and treatment response. Finally, we describe proposed mechanisms of host-microbe interactions that could lead to prostate cancer development, progression or treatment response.
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83
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Advances in Microbiome-Derived Solutions and Methodologies Are Founding a New Era in Skin Health and Care. Pathogens 2022; 11:pathogens11020121. [PMID: 35215065 PMCID: PMC8879973 DOI: 10.3390/pathogens11020121] [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: 10/25/2021] [Revised: 01/11/2022] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
The microbiome, as a community of microorganisms and their structural elements, genomes, metabolites/signal molecules, has been shown to play an important role in human health, with significant beneficial applications for gut health. Skin microbiome has emerged as a new field with high potential to develop disruptive solutions to manage skin health and disease. Despite an incomplete toolbox for skin microbiome analyses, much progress has been made towards functional dissection of microbiomes and host-microbiome interactions. A standardized and robust investigation of the skin microbiome is necessary to provide accurate microbial information and set the base for a successful translation of innovations in the dermo-cosmetic field. This review provides an overview of how the landscape of skin microbiome research has evolved from method development (multi-omics/data-based analytical approaches) to the discovery and development of novel microbiome-derived ingredients. Moreover, it provides a summary of the latest findings on interactions between the microbiomes (gut and skin) and skin health/disease. Solutions derived from these two paths are used to develop novel microbiome-based ingredients or solutions acting on skin homeostasis are proposed. The most promising skin and gut-derived microbiome interventional strategies are presented, along with regulatory, safety, industrial, and technical challenges related to a successful translation of these microbiome-based concepts/technologies in the dermo-cosmetic industry.
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84
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Abstract
Cardiovascular diseases (CVDs) still remain the leading concern of global health, accounting for approximately 17.9 million deaths in 2016. The pathogenetic mechanisms of CVDs are multifactorial and incompletely understood. Recent evidence has shown that alterations in the gut microbiome and its associated metabolites may influence the pathogenesis and progression of CVDs such as atherosclerosis, heart failure, hypertension, and arrhythmia, yet the underlying links are not fully elucidated. Owing to the progress in next-generation sequencing techniques and computational strategies, researchers now are available to explore the emerging links to the genomes, transcriptomes, proteomes, and metabolomes in parallel meta-omics approaches, presenting a panoramic vista of culture-independent microbial investigation. This review aims to outline the characteristics of meta-omics pipelines and provide a brief overview of current applications in CVDs studies which can be practical for addressing crucial knowledge gaps in this field, as well as to shed its light on cardiovascular risk biomarkers and therapeutic intervention in the near future.
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Affiliation(s)
- Jing Xu
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital & National Center for Cardiovascular Diseases, Beijing, China,Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Yuejin Yang
- State Key Laboratory of Cardiovascular Diseases, Fuwai Hospital & National Center for Cardiovascular Diseases, Beijing, China,Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China,CONTACT Yuejin Yang State Key Laboratory of Cardiovascular Disease, Fuwai Hospital & National Center for Cardiovascular Disease, Beijing, China; Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
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85
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Abstract
Environmental chemicals can alter gut microbial community composition, known as dysbiosis. However, the gut microbiota is a highly dynamic system and its functions are still largely underexplored. Likewise, it is unclear whether xenobiotic exposure affects host health through impairing host-microbiota interactions. Answers to this question not only can lead to a more precise understanding of the toxic effects of xenobiotics but also can provide new targets for the development of new therapeutic strategies. Here, we aim to identify the major challenges in the field of microbiota-exposure research and highlight the need to exam the health effects of xenobiotic-induced gut microbiota dysbiosis in host bodies. Although the changes of gut microbiota frequently co-occur with the xenobiotic exposure, the causal relationship of xenobiotic-induced microbiota dysbiosis and diseases is rarely established. The high dynamics of the gut microbiota and the complex interactions among exposure, microbiota, and host, are the major challenges to decipher the specific health effects of microbiota dysbiosis. The next stage of study needs to combine various technologies to precisely assess the xenobiotic-induced gut microbiota perturbation and the subsequent health effects in host bodies. The exposure, gut microbiota dysbiosis, and disease outcomes have to be causally linked. Many microbiota-host interactions are established by previous studies, including signaling metabolites and response pathways in the host, which may use as start points for future research to examine the mechanistic interactions of exposure, gut microbiota, and host health. In conclusion, to precisely understand the toxicity of xenobiotics and develop microbiota-based therapies, the causal and mechanistic links of exposure and microbiota dysbiosis have to be established in the next stage study.
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Affiliation(s)
- Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States
| | - Hongyu Ru
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC, United States,CONTACT Kun Lu Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, NC27599, United States
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86
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Boeri L, Donnaloja F, Campanile M, Sardelli L, Tunesi M, Fusco F, Giordano C, Albani D. Using integrated meta-omics to appreciate the role of the gut microbiota in epilepsy. Neurobiol Dis 2022; 164:105614. [PMID: 35017031 DOI: 10.1016/j.nbd.2022.105614] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/16/2022] Open
Abstract
The way the human microbiota may modulate neurological pathologies is a fascinating matter of research. Epilepsy is a common neurological disorder, which has been largely investigated in correlation with microbiota health and function. However, the mechanisms that regulate this apparent connection are scarcely defined, and extensive effort has been conducted to understand the role of microbiota in preventing and reducing epileptic seizures. Intestinal bacteria seem to modulate the seizure frequency mainly by releasing neurotransmitters and inflammatory mediators. In order to elucidate the complex microbial contribution to epilepsy pathophysiology, integrated meta-omics could be pivotal. In fact, the combination of two or more meta-omics approaches allows a multifactorial study of microbial activity within the frame of disease or drug treatments. In this review, we provide information depicting and supporting the use of multi-omics to study the microbiota-epilepsy connection. We described different meta-omics analyses (metagenomics, metatranscriptomics, metaproteomics and metabolomics), focusing on current technical challenges in stool collection procedures, sample extraction methods and data processing. We further discussed the current advantages and limitations of using the integrative approach of multi-omics in epilepsy investigations.
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Affiliation(s)
- Lucia Boeri
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Francesca Donnaloja
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marzia Campanile
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Lorenzo Sardelli
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Marta Tunesi
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Federica Fusco
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Carmen Giordano
- Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Diego Albani
- Department of Neuroscience, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milan, Italy.
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87
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Guo C, Shi Y. Editorial: Intestinal Microbiota in the Pathogenesis and Management of Necrotizing Enterocolitis in Preterm Infants. Front Pediatr 2022; 10:837925. [PMID: 35252069 PMCID: PMC8892253 DOI: 10.3389/fped.2022.837925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/03/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Chunbao Guo
- Department of Pediatric General Surgery, Children's Hospital of Chongqing Medical University, Chongqing, China.,Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Yuan Shi
- Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.,China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Pediatrics, Children's Hospital of Chongqing Medical University, Chongqing, China.,Department of Neonatology, Chongqing Medical University, Chongqing, China
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88
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Turjeman S, Koren O. Using the microbiome in clinical practice. Microb Biotechnol 2022; 15:129-134. [PMID: 34767683 PMCID: PMC8719822 DOI: 10.1111/1751-7915.13971] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 10/31/2021] [Indexed: 12/13/2022] Open
Affiliation(s)
| | - Omry Koren
- Azrieli Faculty of MedicineBar‐Ilan UniversitySafedIsrael
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89
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Zagury-Orly I, Khaouam N, Noujaim J, Desrosiers MY, Maniakas A. The Effect of Radiation and Chemoradiation Therapy on the Head and Neck Mucosal Microbiome: A Review. Front Oncol 2021; 11:784457. [PMID: 34926301 PMCID: PMC8674486 DOI: 10.3389/fonc.2021.784457] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/11/2021] [Indexed: 12/12/2022] Open
Abstract
Radiation (RT) and chemoradiation therapy (CRT) play an essential role in head and neck cancer treatment. However, both cause numerous side effects in the oral cavity, paranasal sinuses, and pharynx, having deleterious consequences on patients’ quality of life. Concomitant with significant advances in radiation oncology, much attention has turned to understanding the role of the microbiome in the pathogenesis of treatment-induced tissue toxicity, to ultimately explore microbiome manipulation as a therapeutic intervention. This review sought to discuss current publications investigating the impact of RT and CRT-induced changes on the head and neck microbiome, using culture-independent molecular methods, and propose opportunities for future directions. Based on 13 studies derived from a MEDLINE, EMBASE, and Web of Science search on November 7, 2021, use of molecular methods has uncovered various phyla and genera in the head and neck microbiome, particularly the oral microbiome, not previously known using culture-based methods. However, limited research has investigated the impact of RT/CRT on subsites other than the oral cavity and none of the studies aimed to examine the relationship between the head and neck microbiome and treatment effectiveness. Findings from this review provide helpful insights on our current understanding of treatment-induced oral mucositis, dental plaque, and caries formation and highlight the need for future research to examine the effect of RT/CRT on the sinonasal and oropharyngeal microbiome. In addition, future research should use larger cohorts, examine the impact of the microbiome on treatment response, and study the effect of manipulating the microbiome to overcome therapy resistance.
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Affiliation(s)
- Ivry Zagury-Orly
- Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
| | - Nader Khaouam
- Department of Radiation Oncology, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Jonathan Noujaim
- Department of Oncology, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
| | - Martin Y Desrosiers
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada.,Division of Otolaryngology-Head and Neck Surgery, Centre Hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Anastasios Maniakas
- Division of Otolaryngology-Head and Neck Surgery, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada.,Department of Experimental Surgery, McGill University, Montreal, QC, Canada.,Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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90
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Van Den Bossche T, Arntzen MØ, Becher D, Benndorf D, Eijsink VGH, Henry C, Jagtap PD, Jehmlich N, Juste C, Kunath BJ, Mesuere B, Muth T, Pope PB, Seifert J, Tanca A, Uzzau S, Wilmes P, Hettich RL, Armengaud J. The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes. MICROBIOME 2021; 9:243. [PMID: 34930457 PMCID: PMC8690404 DOI: 10.1186/s40168-021-01176-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/10/2021] [Indexed: 05/04/2023]
Abstract
Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.org), the goal of which is to promote dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research. The Initiative aims to be the central information hub and open meeting place where newcomers and experts interact to communicate, standardize, and accelerate experimental and bioinformatic methodologies in this field. We invite the entire microbiome community to join and discuss potential synergies at the interfaces with other disciplines, and to collectively promote innovative approaches to gain deeper insights into microbiome functions and dynamics. Video Abstract.
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Affiliation(s)
- Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000, Ghent, Belgium
| | - Magnus Ø Arntzen
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Dörte Becher
- Institute for Microbiology, Department for Microbial Proteomics, University of Greifswald, 17498, Greifswald, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, 39106, Magdeburg, Germany
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- Microbiology, Anhalt University of Applied Sciences, 06354, Köthen, Germany
| | - Vincent G H Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Céline Henry
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church Street SE, Minneapolis, MN, 55455, USA
| | - Nico Jehmlich
- Helmholtz-Centre for Environmental Research GmbH-UFZ, Department of Molecular Systems Biology, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Catherine Juste
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Benoit J Kunath
- Luxembourg Centre for Systems Biomedicine and Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Bart Mesuere
- VIB-UGent Center for Medical Biotechnology, VIB, 9000, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Thilo Muth
- Section eScience (S.3), Federal Institute for Materials Research and Testing, Berlin, Germany
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, NMBU-Norwegian University of Life Sciences, 1432, Ås, Norway
- Faculty of Biosciences, NMBU - Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jana Seifert
- HoLMiR - Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Str. 6-10, 70599, Stuttgart, Germany
| | - Alessandro Tanca
- Center for Research and Education on the Microbiota, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Center for Research and Education on the Microbiota, Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine and Department of Life Sciences and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Robert L Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200, Bagnols-sur-Cèze, France
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91
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Pratt M, Forbes JD, Knox NC, Bernstein CN, Van Domselaar G. Microbiome-Mediated Immune Signaling in Inflammatory Bowel Disease and Colorectal Cancer: Support From Meta-omics Data. Front Cell Dev Biol 2021; 9:716604. [PMID: 34869308 PMCID: PMC8635193 DOI: 10.3389/fcell.2021.716604] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/31/2021] [Indexed: 12/12/2022] Open
Abstract
Chronic intestinal inflammation and microbial dysbiosis are hallmarks of colorectal cancer (CRC) and inflammatory bowel diseases (IBD), such as Crohn’s disease and ulcerative colitis. However, the mechanistic relationship between gut dysbiosis and disease has not yet been fully characterized. Although the “trigger” of intestinal inflammation remains unknown, a wealth of evidence supports the role of the gut microbiome as a mutualistic pseudo-organ that significantly influences intestinal homeostasis and is capable of regulating host immunity. In recent years, culture-independent methods for assessing microbial communities as a whole (termed meta-omics) have grown beyond taxonomic identification and genome characterization (metagenomics) into new fields of research that collectively expand our knowledge of microbiomes. Metatranscriptomics, metaproteomics, and metabolomics are meta-omics techniques that aim to describe and quantify the functional activity of the gut microbiome. Uncovering microbial metabolic contributions in the context of IBD and CRC using these approaches provides insight into how the metabolic microenvironment of the GI tract shapes microbial community structure and how the microbiome, in turn, influences the surrounding ecosystem. Immunological studies in germ-free and wild-type mice have described several host-microbiome interactions that may play a role in autoinflammation. Chronic colitis is a precursor to CRC, and changes in the gut microbiome may be an important link triggering the neoplastic process in chronic colitis. In this review, we describe several microbiome-mediated mechanisms of host immune signaling, such as short-chain fatty acid (SCFA) and bile acid metabolism, inflammasome activation, and cytokine regulation in the context of IBD and CRC, and discuss the supporting role for these mechanisms by meta-omics data.
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Affiliation(s)
- Molly Pratt
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Jessica D Forbes
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Natalie C Knox
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Charles N Bernstein
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada.,IBD Clinical and Research Centre, University of Manitoba, Winnipeg, MB, Canada
| | - Gary Van Domselaar
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada.,National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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92
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Logotheti M, Agioutantis P, Katsaounou P, Loutrari H. Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma. J Pers Med 2021; 11:jpm11121299. [PMID: 34945771 PMCID: PMC8707330 DOI: 10.3390/jpm11121299] [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: 10/15/2021] [Revised: 11/13/2021] [Accepted: 11/24/2021] [Indexed: 12/12/2022] Open
Abstract
Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients' classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes-endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota-host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.
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Affiliation(s)
- Marianthi Logotheti
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, 5 Iroon Polytechniou Str., Zografou Campus, 15780 Athens, Greece
| | - Panagiotis Agioutantis
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
| | - Paraskevi Katsaounou
- Pulmonary Dept First ICU, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, Ipsilantou 45-7, 10675 Athens, Greece;
| | - Heleni Loutrari
- G.P. Livanos and M. Simou Laboratories, 1st Department of Critical Care Medicine & Pulmonary Services, Evangelismos Hospital, Medical School, National Kapodistrian University of Athens, 3 Ploutarchou Str., 10675 Athens, Greece; (M.L.); (P.A.)
- Correspondence:
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93
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Alexander T, Snowden JA, Burman J, Chang HD, Del Papa N, Farge D, Lindsay JO, Malard F, Muraro PA, Nitti R, Salas A, Sharrack B, Mohty M, Greco R. Intestinal Microbiome in Hematopoietic Stem Cell Transplantation For Autoimmune Diseases: Considerations and Perspectives on Behalf of Autoimmune Diseases Working Party (ADWP) of the EBMT. Front Oncol 2021; 11:722436. [PMID: 34745944 PMCID: PMC8569851 DOI: 10.3389/fonc.2021.722436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/07/2021] [Indexed: 12/12/2022] Open
Abstract
Over the past decades, hematopoietic stem cell transplantation (HSCT) has been evolving as specific treatment for patients with severe and refractory autoimmune diseases (ADs), where mechanistic studies have provided evidence for a profound immune renewal facilitating the observed beneficial responses. The intestinal microbiome plays an important role in host physiology including shaping the immune repertoire. The relationships between intestinal microbiota composition and outcomes after HSCT for hematologic diseases have been identified, particularly for predicting the mortality from infectious and non-infectious causes. Furthermore, therapeutic manipulations of the gut microbiota, such as fecal microbiota transplant (FMT), have emerged as promising therapeutic approaches for restoring the functional and anatomical integrity of the intestinal microbiota post-transplantation. Although changes in the intestinal microbiome have been linked to various ADs, studies investigating the effect of intestinal dysbiosis on HSCT outcomes for ADs are scarce and require further attention. Herein, we describe some of the landmark microbiome studies in HSCT recipients and patients with chronic ADs, and discuss the challenges and opportunities of microbiome research for diagnostic and therapeutic purposes in the context of HSCT for ADs.
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Affiliation(s)
- Tobias Alexander
- Department of Rheumatology and Clinical Immunology - Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and the Berlin Institute of Health (BIH), Berlin, Germany.,Deutsches Rheuma-Forschungszentrum (DRFZ Berlin) - a Leibniz Institute, Berlin, Germany
| | - John A Snowden
- Department of Haematology, Sheffield Teaching Hospitals Foundation NHS Trust, Sheffield, United Kingdom.,Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Joachim Burman
- Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | - Hyun-Dong Chang
- Deutsches Rheuma-Forschungszentrum (DRFZ Berlin) - a Leibniz Institute, Berlin, Germany.,Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | | | - Dominique Farge
- Unité de Médecine Interne: (UF 04) CRMR MATHEC, Maladies Auto-Immunes et Thérapie Cellulaire, Paris, France.,Universite de Paris, IRSL, Recherche Clinique Appliquee `à l'´hématologie, Paris, France.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - James O Lindsay
- Centre for Immunobiology, Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, London, United Kingdom
| | - Florent Malard
- Service d'hématologie Clinique et de Thérapie Cellulaire, Hôpital Saint Antoine, APHP, Sorbonne Université, INSERM UMRs 938, Paris, France
| | - Paolo A Muraro
- Department of Brain Sciences, Imperial College London, London, United Kingdom
| | - Rosamaria Nitti
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
| | | | - Basil Sharrack
- Department of Neuroscience, Sheffield Teaching Hospitals NHS, Foundation Trust, Sheffield, United Kingdom.,NIHR Neurosciences Biomedical Research Centre, University of Sheffield, Sheffield, United Kingdom
| | - Mohamad Mohty
- Service d'hématologie Clinique et de Thérapie Cellulaire, Hôpital Saint Antoine, APHP, Sorbonne Université, INSERM UMRs 938, Paris, France
| | - Raffaella Greco
- Unit of Hematology and Bone Marrow Transplantation, IRCCS San Raffaele Scientific Institute, Vita-Salute San Raffaele University, Milan, Italy
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94
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Xue W, Li JJ, Zou Y, Zou B, Wei L. Microbiota and Ocular Diseases. Front Cell Infect Microbiol 2021; 11:759333. [PMID: 34746029 PMCID: PMC8566696 DOI: 10.3389/fcimb.2021.759333] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/06/2021] [Indexed: 12/12/2022] Open
Abstract
Recent advances have identified significant associations between the composition and function of the gut microbiota and various disorders in organ systems other than the digestive tract. Utilizing next-generation sequencing and multiomics approaches, the microbial community that possibly impacts ocular disease has been identified. This review provides an overview of the literature on approaches to microbiota analysis and the roles of commensal microbes in ophthalmic diseases, including autoimmune uveitis, age-related macular degeneration, glaucoma, and other ocular disorders. In addition, this review discusses the hypothesis of the "gut-eye axis" and evaluates the therapeutic potential of targeting commensal microbiota to alleviate ocular inflammation.
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Affiliation(s)
- Wei Xue
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Jing Jing Li
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Yanli Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, Affiliated Foshan Hospital, Southern Medical University, Foshan, China
| | - Bin Zou
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
| | - Lai Wei
- State Key Laboratory of Ophthalmology, Sun Yat-sen University, Guangzhou, China
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95
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Zheng Y, Ran Y, Zhang H, Wang B, Zhou L. The Microbiome in Autoimmune Liver Diseases: Metagenomic and Metabolomic Changes. Front Physiol 2021; 12:715852. [PMID: 34690796 PMCID: PMC8531204 DOI: 10.3389/fphys.2021.715852] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022] Open
Abstract
Recent studies have identified the critical role of microbiota in the pathophysiology of autoimmune liver diseases (AILDs), including autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), and primary sclerosing cholangitis (PSC). Metagenomic studies reveal significant decrease of gut bacterial diversity in AILDs. Although profiles of metagenomic vary widely, Veillonella is commonly enriched in AIH, PBC, and PSC. Apart from gut microbiome, the oral and bile microbiome seem to be associated with these diseases as well. The functional analysis of metagenomics suggests that metabolic pathways changed in the gut microbiome of the patients. Microbial metabolites, including short-chain fatty acids (SCFAs) and microbial bile acid metabolites, have been shown to modulate innate immunity, adaptive immunity, and inflammation. Taken together, the evidence of host–microbiome interactions and in-depth mechanistic studies needs further accumulation, which will offer more possibilities to clarify the mechanisms of AILDs and provide potential molecular targets for the prevention and treatment in the future.
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Affiliation(s)
- Yanping Zheng
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Ying Ran
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongxia Zhang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Bangmao Wang
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China
| | - Lu Zhou
- Department of Gastroenterology and Hepatology, Tianjin Medical University General Hospital, Tianjin, China.,Department of Gastroenterology and Hepatology, Hotan People's Hospital, Xinjiang, China
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97
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Wu R, Ruan XL, Ruan DD, Zhang JH, Wang HL, Zeng QZ, Lu T, Gan YM, Luo JW, Wu JB. Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease. Am J Transl Res 2021; 13:10056-10074. [PMID: 34650681 PMCID: PMC8507064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The gut microbiota can affect human metabolism, immunity, and other biologic pathways through the complex gut-kidney axis (GKA), and in turn participate in the occurrence and development of kidney disease. In this study, 39 patients with stage 4-5 chronic kidney disease (CKD) and 40 healthy individuals were recruited and 16S rDNA sequencing was performed to analyze the V3-V4 conserved regions of their microbiota. A total of 795 operational taxonomic units (OTUs) shared between groups or specific to each group were obtained, among which 255 OTUs with significant differences between the two groups were identified (P<0.05). Adonis differential analysis showed that the diversity of gut microbiota was highly correlated with CKD stages 4-5. Additionally, 61 genera with differences in the two groups were identified (P<0.05) and 111 species with significant differences in the phyla, classes, orders, families, and genera between the two groups were identified (P<0.05). The differential bacterial genera with the greatest contribution were, in descending order: c_Bacteroidia, o_Bacteroidales, p_Bacteroidetes, c_Clostridia, o_Clostridiales, etc. Those with the greatest contribution in stages 4-5 CKD were, in descending order: p_Proteobacteria, f_Enterobacteriaceae, o_Enterobacteriales, c_Gammaproteobacteria, c_Bacilli, etc. The results suggest that the diversity of the microbiota may affect the occurrence, development, and outcome of the terminal stages of CKD.
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Affiliation(s)
- Rong Wu
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fuqing City Hospital Affiliated to Fujian Medical UniversityFuzhou 350001, Fujian, China
| | - Xing-Lin Ruan
- Department of Neurology, Fujian Medical University Union HospitalFuzhou 350001, Fujian, China
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical UniversityFuzhou 350005, Fujian, China
| | - Dan-Dan Ruan
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
| | - Jian-Hui Zhang
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
| | - Han-Lu Wang
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
| | - Quan-Zuan Zeng
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
| | - Tao Lu
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
| | - Yu-Mian Gan
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
| | - Jie-Wei Luo
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
| | - Jia-Bin Wu
- Shengli Clinical Medical College, Fujian Medical UniversityFuzhou 350001, Fujian, China
- Department of Nephrology, Fujian Provincial HospitalFuzhou 350001, Fujian, China
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98
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Eustis SJ, McCall MW, Murphy EA, Wirth MD. Association Between Gastrointestinal Symptoms and Depression in a Representative Sample of Adults in the United States: Findings From National Health and Nutrition Examination Survey (2005-2016). J Acad Consult Liaison Psychiatry 2021; 63:268-279. [PMID: 34461293 DOI: 10.1016/j.jaclp.2021.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/08/2021] [Accepted: 08/15/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND The microbiome's role in the etiology of depression has been a topic of many recent investigations. Findings suggest that dysbiosis, which describes a general disturbance in the gut microbiome, underlies negative gastrointestinal symptoms and is implicated in depression. We studied associations between gastrointestinal symptoms and depressive symptoms at a population level using cross-sectional data from the National Health and Nutrition Examination Survey (2005-2016, n = 36,287). We hypothesized that the odds of depressive symptoms would be significantly higher in those showing signs of gastrointestinal distress. METHODS We analyzed 31,191 adults participating in the National Health and Nutrition Examination Survey from 2005-2016. Outcomes included presence of mucus or liquid in bowel leakage and stomach illness in the past month, diarrhea in the past year, and number of weekly bowel movements. The survey (and thus, our analyses) does not include microbiome samples, only self-reported gastrointestinal symptoms. Depressive symptoms were measured using the Patient Health Questionnaire. Moderate, moderately severe, and severe scores were coded as a positive outcome. RESULTS Compared to those without depressive symptoms, those with moderate-to-severe depressive symptoms had elevated odds of bowel mucus (odds ratio = 2.78; 95% confidence interval = 1.82-4.24), bowel liquid (odds ratio = 2.16; 95% confidence interval = 1.63-2.86), stomach illness (odds ratio = 1.82; 95% confidence interval = 1.31-2.53), diarrhea (sometimes vs. never odds ratio = 1.72; 95% confidence interval = 1.30-2.29), and constipation (sometimes vs. never odds ratio = 2.76; 95% confidence interval = 2.11-3.62). Overall, those with gastrointestinal symptoms were significantly more likely to have depressive symptoms. CONCLUSIONS While the intricacies of the brain-gut axis are being investigated at the molecular level, these population data provide further evidence for the association between depressive symptoms and signs of dysbiosis, which may inform health care providers' patient interactions.
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Affiliation(s)
| | - Michael W McCall
- Department of Psychology, University of South Carolina, Columbia, SC
| | - E Angela Murphy
- Departments of Pathology, Microbiology, and Immunology, School of Medicine, University of South Carolina, Columbia, SC
| | - Michael D Wirth
- Tufts University School of Medicine, Boston, MA; College of Nursing, University of South Carolina, Columbia, SC; Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC
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Zhu G, Du R, Du D, Qian J, Ye M. Keystone taxa shared between earthworm gut and soil indigenous microbial communities collaboratively resist chlordane stress. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 283:117095. [PMID: 33862342 DOI: 10.1016/j.envpol.2021.117095] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/27/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Chlordane is an organochlorine pesticide that is applied extensively. Residual concentrations that remain in soils after application are highly toxic to soil organisms, particularly affecting the earthworm gut and indigenous soil microorganisms. However, response mechanisms of the earthworm gut and indigenous soil microorganism communities to chlordane exposure are not well known. In this study, earthworms (Metaphire guillelmi) were exposed to chlordane-contaminated soils to investigate their response mechanisms over a gradient of chlordane toxicity. Results from high-throughput sequencing and network analysis showed that the bacterial composition in the earthworm gut varied more significantly than that in indigenous soil microbial communities under different concentrations of chlordane stress (2.3-60.8 mg kg-1; p < 0.05). However, keystone species of Flavobacterium, Candidatus Nitrososphaera, and Acinetobacter remained stable in both the earthworm gut and bacterial communities despite varying degrees of chlordane exposure, and their relative abundance was slightly higher in the low-concentration treatment group (T1, T2) than in the high-concentration treatment group (T3, T4). Additionally, network analysis demonstrated that the average value of the mean degree of centrality, closeness centrality, and eigenvector centrality of all keystone species screened by four methods (MetagenomeSeq, LEfSe, OPLS-DA, Random Forest) were 161.3, 0.5, and 0.63, respectively, and that these were significantly higher (p < 0.05) than values for non-keystone species (84.9, 0.4, and 0.2, respectively). Keystone species had greater network connectivity and a stronger capacity to degrade pesticides and transform carbon and nitrogen than non-keystone species. The keystone species, which were closely related to the microbial community in soil indigenous flora and earthworm intestinal flora, could resist chlordane stress and undertake pesticide degradation. These results have increased understanding of the role of the earthworm gut and indigenous soil bacteria in resisting chlordane stress and sustaining microbial equilibrium in soil.
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Affiliation(s)
- Guofan Zhu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China; School of Resources and Environmental Engineering, Hefei University of Technology, Heifei, 230009, PR China
| | - Ruijun Du
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Daolin Du
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, 212013, PR China
| | - Jiazhong Qian
- School of Resources and Environmental Engineering, Hefei University of Technology, Heifei, 230009, PR China
| | - Mao Ye
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, PR China.
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100
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Gilroy R. Spotlight on the avian gut microbiome: fresh opportunities in discovery. Avian Pathol 2021; 50:291-294. [PMID: 34264153 DOI: 10.1080/03079457.2021.1955826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Chickens represent a globally ubiquitous food animal underpinning many aspects of human nutrition and health. Consumption of chicken meat continues to surge, representing a cheaper, healthier, low-carbon alternative to other livestock meats. Despite this importance, we are still unable to define what lives within the chicken gut microbiome. This complex community bridges poultry diet, health and productivity as well as providing a reservoir for zoonotic pathogens. Even with decades of intensive study, we are still discovering novel microbial species within this environment, each of which has the potential to provide an avenue for commercial microbiome modulation. The chicken gut truly represents an exhilarating challenge in turning new-found knowledge into new-won power to improve the health and wealth of poultry and people.
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