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Moutsoglou D, Ramakrishnan P, Vaughn BP. Microbiota transplant therapy in inflammatory bowel disease: advances and mechanistic insights. Gut Microbes 2025; 17:2477255. [PMID: 40062406 PMCID: PMC11901402 DOI: 10.1080/19490976.2025.2477255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2024] [Revised: 01/27/2025] [Accepted: 03/04/2025] [Indexed: 03/14/2025] Open
Abstract
Microbiota transplant therapy is an emerging therapy for inflammatory bowel disease, but factors influencing its efficacy and mechanism remain poorly understood. In this narrative review, we outline key elements affecting therapeutic outcomes, including donor factors (such as age and patient relationship), recipient factors, control selection, and elements impacting engraftment and its correlation with clinical response. We also examine potential mechanisms through inflammatory bowel disease trials, focusing on the interplay between the microbiota, host, and immune system. Finally, we briefly explore potential future directions for microbiota transplant therapy and promising emerging treatments.
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Affiliation(s)
- Daphne Moutsoglou
- Gastroenterology Section, Minneapolis VA Health Care System, Minneapolis, MN, USA
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | | | - Byron P. Vaughn
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, MN, USA
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2
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Hussain M, Aizpurua O, Pérez de Rozas A, París N, Guivernau M, Jofré A, Tous N, Ng'ang'a ZW, Alberdi A, Rodríguez-Gallego E, Kogut MH, Tarradas J. Positive impact of early-probiotic administration on performance parameters, intestinal health and microbiota populations in broiler chickens. Poult Sci 2024; 103:104401. [PMID: 39489036 PMCID: PMC11566344 DOI: 10.1016/j.psj.2024.104401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 10/04/2024] [Accepted: 10/04/2024] [Indexed: 11/05/2024] Open
Abstract
Minimizing the utilization of antibiotics in animal production is crucial to prevent the emergence of antimicrobial resistances. Thus, research on alternatives is needed to maintain productivity, sustainability, and animal health. To gain a comprehensive understanding of probiotics' modes of action on performance, intestinal microbiota, and gut health in poultry, 3 probiotic strains (Enterococcus faecalis CV1028 [EntF], Bacteroides fragilis GP1764 [BacF], and Ligilactobacillus salivarius CTC2197 [LacS]) were tested in 2 in vivo trials. Trial 1 comprised of a negative control group fed basal diet (BD) and 3 treatment groups that received BD with EntF, BacF and LacS. Trial 2 included a negative control group, a positive control group with Zinc-Bacitracin as antibiotic growth promoter (AGP), and 2 groups treated with a blend of probiotics (EntF+BacF+LacS) during 0 to 10 or 0 to 35 d, respectively. Wheat-soybean-rye based diets without exogenous enzymes were used as a challenge model to induce intestinal mild- or moderate-inflammatory process in the gut. In Trial 1, individually administered probiotics improved FCR at 8 d compared to Control, but these positive effects were lost in the following growing periods probably due to the high grade of challenging diet and a too low dose of probiotics. In Trial 2, both Probiotic treatments, administered only 10 or 35 d, significantly improved FCR to the same extent as of the Antibiotic group at the end of the trial. Although the performance between antibiotic and probiotic mixture showed similar values, microbiota analysis revealed different microbial composition at 7 d, but not at 21 d. This suggests that modes of action of the AGP and the tested probiotic blend differ on their effects on microbiome, and that the changes observed during the first days' posthatch are relevant on performance at the end of the study. Therefore, the probiotics administration only during the first 10 d posthatch was proven sufficient to induce similar performance improvements to those observed in birds fed antibiotic growth promoters throughout the whole experimental trial.
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Affiliation(s)
- M Hussain
- IRTA, Animal Nutrition, Mas Bové, 43120 Constantí, Catalonia, Spain; MoBioFood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, c/Marcel·lí Domingo n°1, 43007 Tarragona, Spain
| | - O Aizpurua
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - A Pérez de Rozas
- IRTA, Animal Health, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Catalonia, Spain
| | - N París
- IRTA, Animal Nutrition, Mas Bové, 43120 Constantí, Catalonia, Spain
| | - M Guivernau
- IRTA, Sustainability in Biosystems, Torre Marimón, 08140 Caldes de Montbui, Catalonia, Spain
| | - A Jofré
- IRTA, Food Safety and Functionality, Finca Camps i Armet, 17121 Monells, Catalonia, Spain
| | - N Tous
- IRTA, Animal Nutrition, Mas Bové, 43120 Constantí, Catalonia, Spain
| | - Z W Ng'ang'a
- IRTA, Animal Nutrition, Mas Bové, 43120 Constantí, Catalonia, Spain; MoBioFood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, c/Marcel·lí Domingo n°1, 43007 Tarragona, Spain
| | - A Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - E Rodríguez-Gallego
- MoBioFood Research Group, Department of Biochemistry and Biotechnology, Universitat Rovira i Virgili, c/Marcel·lí Domingo n°1, 43007 Tarragona, Spain
| | - M H Kogut
- Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, USA
| | - J Tarradas
- IRTA, Animal Nutrition, Mas Bové, 43120 Constantí, Catalonia, Spain.
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3
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Hameleers L, Gaenssle LA, Bertran‐Llorens S, Pijning T, Jurak E. Polysaccharide utilization loci encoded DUF1735 likely functions as membrane-bound spacer for carbohydrate active enzymes. FEBS Open Bio 2024; 14:1133-1146. [PMID: 38735878 PMCID: PMC11216935 DOI: 10.1002/2211-5463.13816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/17/2024] [Accepted: 04/29/2024] [Indexed: 05/14/2024] Open
Abstract
Proteins featuring the Domain of Unknown Function 1735 are frequently found in Polysaccharide Utilization Loci, yet their role remains unknown. The domain and vicinity analyzer programs we developed mine the Kyoto Encyclopedia of Genes and Genomes and UniProt to enhance the functional prediction of DUF1735. Our datasets confirmed the exclusive presence of DUF1735 in Bacteroidota genomes, with Bacteroidetes thetaiotaomicron harboring 46 copies. Notably, 97.8% of DUF1735 are encoded in PULs, and 89% are N-termini of multimodular proteins featuring C-termini like Laminin_G_3, F5/8-typeC, and GH18 domains. Predominantly possessing a predicted lipoprotein signal peptide and sharing an immunoglobulin-like β-sandwich fold with the BACON domain and the N-termini of SusE/F, DUF1735 likely functions as N-terminal, membrane-bound spacer for diverse C-termini involved in PUL-mediated carbohydrate utilization.
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Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct EngineeringUniversity of GroningenThe Netherlands
| | - Lucie A. Gaenssle
- Department of Bioproduct EngineeringUniversity of GroningenThe Netherlands
| | | | - Tjaard Pijning
- Department of Biomolecular X‐ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenThe Netherlands
| | - Edita Jurak
- Department of Bioproduct EngineeringUniversity of GroningenThe Netherlands
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4
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Buzun E, Hsu CY, Sejane K, Oles RE, Vasquez Ayala A, Loomis LR, Zhao J, Rossitto LA, McGrosso DM, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early-life colonization by a pioneering gut commensal. Cell Host Microbe 2024; 32:181-190.e9. [PMID: 38228143 PMCID: PMC10922750 DOI: 10.1016/j.chom.2023.12.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/14/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024]
Abstract
The early microbial colonization of the gastrointestinal tract can have long-term impacts on development and health. Keystone species, including Bacteroides spp., are prominent in early life and play crucial roles in maintaining the structure of the intestinal ecosystem. However, the process by which a resilient community is curated during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa in early life and regulates a commensal colonization program. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. NanH is required for vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and microbiota mediated through host-derived glycans to promote stable colonization.
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Affiliation(s)
- Ekaterina Buzun
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kristija Sejane
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Adriana Vasquez Ayala
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiaqi Zhao
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Leigh-Ana Rossitto
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dominic M McGrosso
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA
| | - David J Gonzalez
- Department of Pharmacology, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Lars Bode
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Larsson-Rosenquist Foundation Mother-Milk-Infant Center of Research Excellence (MOMI CORE), University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Human Milk Institute (HMI), University of California, San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA 92093, USA; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON M5G 1M1, Canada.
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5
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Moran CL, Debowski A, Vrielink A, Stubbs K, Sarkar-Tyson M. N-acetyl-β-hexosaminidase activity is important for chitooligosaccharide metabolism and biofilm formation in Burkholderia pseudomallei. Environ Microbiol 2024; 26:e16571. [PMID: 38178319 DOI: 10.1111/1462-2920.16571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/18/2023] [Indexed: 01/06/2024]
Abstract
Burkholderia pseudomallei is a saprophytic Gram-negative bacillus that can cause the disease melioidosis. Although B. pseudomallei is a recognised member of terrestrial soil microbiomes, little is known about its contribution to the saprophytic degradation of polysaccharides within its niche. For example, while chitin is predicted to be abundant within terrestrial soils the chitinolytic capacity of B. pseudomallei is yet to be defined. This study identifies and characterises a putative glycoside hydrolase, bpsl0500, which is expressed by B. pseudomallei K96243. Recombinant BPSL0500 was found to exhibit activity against substrate analogues and GlcNAc disaccharides relevant to chitinolytic N-acetyl-β-d-hexosaminidases. In B. pseudomallei, bpsl0500 was found to be essential for both N-acetyl-β-d-hexosaminidase activity and chitooligosaccharide metabolism. Furthermore, bpsl0500 was also observed to significantly affect biofilm deposition. These observations led to the identification of BPSL0500 activity against model disaccharide linkages that are present in biofilm exopolysaccharides, a feature that has not yet been described for chitinolytic enzymes. The results in this study indicate that chitinolytic N-acetyl-β-d-hexosaminidases like bpsl0500 may facilitate biofilm disruption as well as chitin assimilation, providing dual functionality for saprophytic bacteria such as B. pseudomallei within the competitive soil microbiome.
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Affiliation(s)
- Clare L Moran
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Aleksandra Debowski
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
| | - Keith Stubbs
- School of Molecular Sciences, The University of Western Australia, Crawley, Australia
- ARC Training Centre for Next-Gen Technologies in Biomedical Analysis, School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Mitali Sarkar-Tyson
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
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6
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Xue H, Mei C, Wang F, Tang X. Relationship among Chinese herb polysaccharide (CHP), gut microbiota, and chronic diarrhea and impact of CHP on chronic diarrhea. Food Sci Nutr 2023; 11:5837-5855. [PMID: 37823142 PMCID: PMC10563694 DOI: 10.1002/fsn3.3596] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/13/2023] [Accepted: 07/22/2023] [Indexed: 10/13/2023] Open
Abstract
Chronic diarrhea, including diarrhea-predominant irritable bowel syndrome (IBS-D), osmotic diarrhea, bile acid diarrhea, and antibiotic-associated diarrhea, is a common problem which is highly associated with disorders of the gut microbiota composition such as small intestinal bacterial overgrowth (SIBO) and so on. A growing number of studies have supported the view that Chinese herbal formula alleviates the symptoms of diarrhea by modulating the fecal microbiota. Chinese herbal polysaccharides (CHPs) are natural polymers composed of monosaccharides that are widely found in Chinese herbs and function as important active ingredients. Commensal gut microbiota has an extensive capacity to utilize CHPs and play a vital role in degrading polysaccharides into short-chain fatty acids (SCFAs). Many CHPs, as prebiotics, have an antidiarrheal role to promote the growth of beneficial bacteria and inhibit the colonization of pathogenic bacteria. This review systematically summarizes the relationship among gut microbiota, chronic diarrhea, and CHPs as well as recent progress on the impacts of CHPs on the gut microbiota and recent advances on the possible role of CHPs in chronic diarrhea.
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Affiliation(s)
- Hong Xue
- Digestive Laboratory of Traditional Chinese Medicine Research Institute of Spleen and Stomach DiseasesXiyuan Hospital, China Academy of Chinese Medical SciencesBeijingChina
| | - Chun‐Feng Mei
- Digestive Laboratory of Traditional Chinese Medicine Research Institute of Spleen and Stomach DiseasesXiyuan Hospital, China Academy of Chinese Medical SciencesBeijingChina
| | - Feng‐Yun Wang
- Digestive Laboratory of Traditional Chinese Medicine Research Institute of Spleen and Stomach DiseasesXiyuan Hospital, China Academy of Chinese Medical SciencesBeijingChina
| | - Xu‐Dong Tang
- Digestive Laboratory of Traditional Chinese Medicine Research Institute of Spleen and Stomach DiseasesXiyuan Hospital, China Academy of Chinese Medical SciencesBeijingChina
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7
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Neal M, Thiruppathy D, Zengler K. Genome-scale metabolic modeling of the human gut bacterium Bacteroides fragilis strain 638R. PLoS Comput Biol 2023; 19:e1011594. [PMID: 37903176 PMCID: PMC10635569 DOI: 10.1371/journal.pcbi.1011594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 11/09/2023] [Accepted: 10/11/2023] [Indexed: 11/01/2023] Open
Abstract
Bacteroides fragilis is a universal member of the dominant commensal gut phylum Bacteroidetes. Its fermentation products and abundance have been linked to obesity, inflammatory bowel disease, and other disorders through its effects on host metabolic regulation and the immune system. As of yet, there has been no curated systems-level characterization of B. fragilis' metabolism that provides a comprehensive analysis of the link between human diet and B. fragilis' metabolic products. To address this, we developed a genome-scale metabolic model of B. fragilis strain 638R. The model iMN674 contains 1,634 reactions, 1,362 metabolites, three compartments, and reflects the strain's ability to utilize 142 metabolites. Predictions made with this model include its growth rate and efficiency on these substrates, the amounts of each fermentation product it produces under different conditions, and gene essentiality for each biomass component. The model highlights and resolves gaps in knowledge of B. fragilis' carbohydrate metabolism and its corresponding transport proteins. This high quality model provides the basis for rational prediction of B. fragilis' metabolic interactions with its environment and its host.
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Affiliation(s)
- Maxwell Neal
- Department of Bioengineering, University of California, San Diego, California, United States of America
| | - Deepan Thiruppathy
- Department of Bioengineering, University of California, San Diego, California, United States of America
| | - Karsten Zengler
- Department of Bioengineering, University of California, San Diego, California, United States of America
- Department of Pediatrics, University of California, San Diego, California, United States of America
- Center for Microbiome Innovation, University of California, San Diego, California, United States of America
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8
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Bains RK, Nasseri SA, Liu F, Wardman JF, Rahfeld P, Withers SG. Characterization of a new family of 6-sulfo-N-acetylglucosaminidases. J Biol Chem 2023; 299:105214. [PMID: 37660924 PMCID: PMC10570127 DOI: 10.1016/j.jbc.2023.105214] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
Sulfation is widespread in nature and plays an important role in modulating biological function. Among the strategies developed by microbes to access sulfated oligosaccharides as a nutrient source is the production of 6-sulfoGlcNAcases to selectively release 6-sulfoGlcNAc from target oligosaccharides. Thus far, all 6-sulfoGlcNAcases identified have belonged to the large GH20 family of β-hexosaminidases. Ηere, we identify and characterize a new, highly specific non-GH20 6-sulfoGlcNAcase from Streptococcus pneumoniae TIGR4, Sp_0475 with a greater than 110,000-fold preference toward N-acetyl-β-D-glucosamine-6-sulfate substrates over the nonsulfated version. Sp_0475 shares distant sequence homology with enzymes of GH20 and with the newly formed GH163 family. However, the sequence similarity between them is sufficiently low that Sp_0475 has been assigned as the founding member of a new glycoside hydrolase family, GH185. By combining results from site-directed mutagenesis with mechanistic studies and bioinformatics we provide insight into the substrate specificity, mechanism, and key active site residues of Sp_0475. Enzymes of the GH185 family follow a substrate-assisted mechanism, consistent with their distant homology to the GH20 family, but the catalytic residues involved are quite different. Taken together, our results highlight in more detail how microbes can degrade sulfated oligosaccharides for nutrients.
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Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seyed A Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacob F Wardman
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
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9
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Buzun E, Hsu CY, Sejane K, Oles RE, Ayala AV, Loomis LR, Zhao J, Rossitto LA, McGrosso D, Gonzalez DJ, Bode L, Chu H. A bacterial sialidase mediates early life colonization by a pioneering gut commensal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552477. [PMID: 37609270 PMCID: PMC10441351 DOI: 10.1101/2023.08.08.552477] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
The early microbial colonization of the gastrointestinal tract can lead to long-term impacts in development and overall human health. Keystone species, including Bacteroides spp ., play a crucial role in maintaining the structure, diversity, and function of the intestinal ecosystem. However, the process by which a defined and resilient community is curated and maintained during early life remains inadequately understood. Here, we show that a single sialidase, NanH, in Bacteroides fragilis mediates stable occupancy of the intestinal mucosa and regulates the commensal colonization program during the first weeks of life. This program is triggered by sialylated glycans, including those found in human milk oligosaccharides and intestinal mucus. After examining the dynamics between pioneer gut Bacteroides species in the murine gut, we discovered that NanH enables vertical transmission from dams to pups and promotes B. fragilis dominance during early life. Furthermore, we demonstrate that NanH facilitates commensal resilience and recovery after antibiotic treatment in a defined microbial community. Collectively, our study reveals a co-evolutionary mechanism between the host and the microbiota mediated through host-derived glycans to promote stable intestinal colonization.
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10
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Yamaguchi M, Yamamoto K. Mucin glycans and their degradation by gut microbiota. Glycoconj J 2023; 40:493-512. [PMID: 37318672 DOI: 10.1007/s10719-023-10124-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/13/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
The human intestinal tract is inhabited by a tremendous number of microorganisms, which are collectively termed "the gut microbiota". The intestinal epithelium is covered with a dense layer of mucus that prevents penetration of the gut microbiota into underlying tissues of the host. Recent studies have shown that the maturation and function of the mucus layer are strongly influenced by the gut microbiota, and alteration in the structure and function of the gut microbiota is implicated in several diseases. Because the intestinal mucus layer is at a crucial interface between microbes and their host, its breakdown leads to gut bacterial invasion that can eventually cause inflammation and infection. The mucus is composed of mucin, which is rich in glycans, and the various structures of the complex carbohydrates of mucins can select for distinct mucosa-associated bacteria that are able to bind mucin glycans, and sometimes degrade them as a nutrient source. Mucin glycans are diverse molecules, and thus mucin glycan degradation is a complex process that requires a broad range of glycan-degrading enzymes. Because of the increased recognition of the role of mucus-associated microbes in human health, how commensal bacteria degrade and use host mucin glycans has become of increased interest. This review provides an overview of the relationships between the mucin glycan of the host and gut commensal bacteria, with a focus on mucin degradation.
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Affiliation(s)
- Masanori Yamaguchi
- Department of Organic Bio Chemistry, Faculty of Education, Wakayama University, 930, Sakaedani, Wakayama, 640-8510, Japan.
| | - Kenji Yamamoto
- Center for Innovative and Joint Research, Wakayama University, 930, Sakaedani, Wakayama, 640-8510, Japan
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Panwar D, Shubhashini A, Kapoor M. Complex alpha and beta mannan foraging by the human gut bacteria. Biotechnol Adv 2023; 66:108166. [PMID: 37121556 DOI: 10.1016/j.biotechadv.2023.108166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
The human gut microbiota (HGM), a community of trillions of microbes, underscores its contribution by impacting many facets of host health and disease. In the HGM, Bacteroidota and Bacillota represent dominant bacterial phyla, which mainly rely on the glycans recalcitrant to host digestion to meet their energy requirements. Accordingly, the impact of dietary and host-derived glycans in the assembly and operation of these dominant microbial communities continues to be an area of active research. Among various glycans, mannans represent an integral component of the human diet. Apart from their health effects, the diverse and complex mannan structures bears molecular signatures that alter the expression of specific gene clusters in selected Bacteroidota and Bacillota species. Both the phyla possess variable and sophisticated loci of mannan recognition proteins, hydrolytic enzymes, transporters, and other metabolic proteins to sense, capture and utilize mannans as an energy source. The current review summarizes mannan structural diversity, and strategies adopted by select species of the HGM bacteria to forage mannans by focusing primarily on glycoside hydrolases and their effects on host health and metabolism.
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Affiliation(s)
- Deepesh Panwar
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India
| | - A Shubhashini
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India
| | - Mukesh Kapoor
- Department of Microbiology and Fermentation Technology, CSIR-Central Food Technological Research Institute, Mysuru 570 020, India; Academy of Scientific and Innovative Research (AcSIR), CSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Ghaziabad, UP 201 002, India.
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12
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Abstract
N-glycans are common posttranslational modifications on plant proteins, particularly secreted proteins. As plants are the major component of the human diet, and especially in high-fiber diets, plant N-glycans are prominent in the gut. Despite their ubiquity in the gut, the degradation of plant N-glycans by the microbiota has not been described. Here we used a functional analysis approach, coupled to detailed biochemistry and structural biology, to reveal a pathway for the degradation of plant N-glycans encoded by the human gut microbiota. The work reveals insight into how our gut microbes use plant N-glycans as a nutrient source and also provides tools to modify plant N-glycans to mitigate allergic responses, either from foods or plant-expressed therapeutics. The major nutrients available to the human colonic microbiota are complex glycans derived from the diet. To degrade this highly variable mix of sugar structures, gut microbes have acquired a huge array of different carbohydrate-active enzymes (CAZymes), predominantly glycoside hydrolases, many of which have specificities that can be exploited for a range of different applications. Plant N-glycans are prevalent on proteins produced by plants and thus components of the diet, but the breakdown of these complex molecules by the gut microbiota has not been explored. Plant N-glycans are also well characterized allergens in pollen and some plant-based foods, and when plants are used in heterologous protein production for medical applications, the N-glycans present can pose a risk to therapeutic function and stability. Here we use a novel genome association approach for enzyme discovery to identify a breakdown pathway for plant complex N-glycans encoded by a gut Bacteroides species and biochemically characterize five CAZymes involved, including structures of the PNGase and GH92 α-mannosidase. These enzymes provide a toolbox for the modification of plant N-glycans for a range of potential applications. Furthermore, the keystone PNGase also has activity against insect-type N-glycans, which we discuss from the perspective of insects as a nutrient source.
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13
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Cheng J, Hu J, Geng F, Nie S. Bacteroides utilization for dietary polysaccharides and their beneficial effects on gut health. FOOD SCIENCE AND HUMAN WELLNESS 2022. [DOI: 10.1016/j.fshw.2022.04.002] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Abstract
Secretory immunoglobulin A (SIgA) in human milk plays a central role in complex maternal-infant interactions that influence long-term health outcomes. Governed by genetics and maternal microbial exposure, human milk SIgA shapes both the microbiota and immune system of infants. Historically, SIgA-microbe interactions have been challenging to unravel due to their dynamic and personalized nature, particularly during early life. Recent advances have helped to clarify how SIgA acts beyond simple pathogen clearance to help guide and constrain a healthy microbiota, promote tolerance, and influence immune system development. In this review, we highlight these new findings in the context of the critical early-life window and propose outstanding areas of study that will be key to harnessing the benefits of SIgA to support healthy immune development during infancy.
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15
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Wardman JF, Bains RK, Rahfeld P, Withers SG. Carbohydrate-active enzymes (CAZymes) in the gut microbiome. Nat Rev Microbiol 2022; 20:542-556. [PMID: 35347288 DOI: 10.1038/s41579-022-00712-1] [Citation(s) in RCA: 270] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
Abstract
The 1013-1014 microorganisms present in the human gut (collectively known as the human gut microbiota) dedicate substantial percentages of their genomes to the degradation and uptake of carbohydrates, indicating the importance of this class of molecules. Carbohydrates function not only as a carbon source for these bacteria but also as a means of attachment to the host, and a barrier to infection of the host. In this Review, we focus on the diversity of carbohydrate-active enzymes (CAZymes), how gut microorganisms use them for carbohydrate degradation, the different chemical mechanisms of these CAZymes and the roles that these microorganisms and their CAZymes have in human health and disease. We also highlight examples of how enzymes from this treasure trove have been used in manipulation of the microbiota for improved health and treatment of disease, in remodelling the glycans on biopharmaceuticals and in the potential production of universal O-type donor blood.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rajneesh K Bains
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. .,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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16
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Microbiomes in the Intestine of Developing Pigs: Implications for Nutrition and Health. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1354:161-176. [PMID: 34807442 DOI: 10.1007/978-3-030-85686-1_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The past decade has seen an expansion of studies on the role of gut microbiome in piglet nutrition and health. With the help of culture-independent sequencing techniques, the colonization of gut microbiota and their implication in physiology are being investigated in depth. Immediately after birth, the microbes begin to colonize following an age-dependent trajectory, which can be modified by maternal environment, diet, antibiotics, and fecal microbiota transplantation. The early-life gut microbiome is relatively simple but enriched with huge metabolic potential to utilize milk oligosaccharides and affect the epithelial function. After weaning, the gut microbiome develops towards a gradual adaptation to the introduction of solid food, with an enhanced ability to metabolize amino acids, fibers, and bile acids. Here we summarize the compositional and functional difference of the gut microbiome in the keystone developing phases, with a specific focus on the use of different nutritional approaches based on the phase-specific gut microbiome.
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17
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Analysis of six tonB gene homologs in Bacteroides fragilis revealed that tonB3 is essential for survival in experimental intestinal colonization and intra-abdominal infection. Infect Immun 2021; 90:e0046921. [PMID: 34662212 DOI: 10.1128/iai.00469-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The opportunistic, anaerobic pathogen and commensal of the human large intestinal tract, Bacteroides fragilis strain 638R, contains six predicted TonB proteins, termed TonB1-6, four ExbBs orthologs, ExbB1-4, and five ExbDs orthologs, ExbD1-5. The inner membrane TonB/ExbB/ExbD complex harvests energy from the proton motive force (Δp) and the TonB C-terminal domain interacts with and transduces energy to outer membrane TonB-dependent transporters (TBDTs). However, TonB's role in activating nearly one hundred TBDTs for nutrient acquisition in B. fragilis during intestinal colonization and extraintestinal infection has not been established. In this study, we show that growth was abolished in the ΔtonB3 mutant when heme, vitamin B12, Fe(III)-ferrichrome, starch, mucin-glycans, or N-linked glycans were used as a substrate for growth in vitro. Genetic complementation of the ΔtonB3 mutant with the tonB3 gene restored growth on these substrates. The ΔtonB1, ΔtonB2, ΔtonB4, ΔtonB5, and ΔtonB6 single mutants did not show a growth defect. This indicates that there was no functional compensation for the lack of TonB3, and it demonstrates that TonB3, alone, drives the TBDTs involved in the transport of essential nutrients. The ΔtonB3 mutant had a severe growth defect in a mouse model of intestinal colonization compared to the parent strain. This intestinal growth defect was enhanced in the ΔtonB3 ΔtonB6 double mutant strain which completely lost its ability to colonize the mouse intestinal tract compared to the parent strain. The ΔtonB1, ΔtonB2, ΔtonB4, and ΔtonB5 mutants did not significantly affect intestinal colonization. Moreover, the survival of the ΔtonB3 mutant strain was completely eradicated in a rat model of intra-abdominal infection. Taken together, these findings show that TonB3 was essential for survival in vivo. The genetic organization of tonB1, tonB2, tonB4, tonB5, and tonB6 gene orthologs indicates that they may interact with periplasmic and nonreceptor outer membrane proteins, but the physiological relevance of this has not been defined. Because anaerobic fermentation metabolism yields a lower Δp than aerobic respiration and B. fragilis has a reduced redox state in its periplasmic space - in contrast to an oxidative environment in aerobes - it remains to be determined if the diverse system of TonB/ExbB/ExbD orthologs encoded by B. fragilis have an increased sensitivity to PMF (relative to aerobic bacteria) to allow for the harvesting of energy under anaerobic conditions.
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18
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Giron LB, Dweep H, Yin X, Wang H, Damra M, Goldman AR, Gorman N, Palmer CS, Tang HY, Shaikh MW, Forsyth CB, Balk RA, Zilberstein NF, Liu Q, Kossenkov A, Keshavarzian A, Landay A, Abdel-Mohsen M. Plasma Markers of Disrupted Gut Permeability in Severe COVID-19 Patients. Front Immunol 2021; 12:686240. [PMID: 34177935 PMCID: PMC8219958 DOI: 10.3389/fimmu.2021.686240] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/10/2021] [Indexed: 12/15/2022] Open
Abstract
A disruption of the crosstalk between the gut and the lung has been implicated as a driver of severity during respiratory-related diseases. Lung injury causes systemic inflammation, which disrupts gut barrier integrity, increasing the permeability to gut microbes and their products. This exacerbates inflammation, resulting in positive feedback. We aimed to test whether severe Coronavirus disease 2019 (COVID-19) is associated with markers of disrupted gut permeability. We applied a multi-omic systems biology approach to analyze plasma samples from COVID-19 patients with varying disease severity and SARS-CoV-2 negative controls. We investigated the potential links between plasma markers of gut barrier integrity, microbial translocation, systemic inflammation, metabolome, lipidome, and glycome, and COVID-19 severity. We found that severe COVID-19 is associated with high levels of markers of tight junction permeability and translocation of bacterial and fungal products into the blood. These markers of disrupted intestinal barrier integrity and microbial translocation correlate strongly with higher levels of markers of systemic inflammation and immune activation, lower levels of markers of intestinal function, disrupted plasma metabolome and glycome, and higher mortality rate. Our study highlights an underappreciated factor with significant clinical implications, disruption in gut functions, as a potential force that may contribute to COVID-19 severity.
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Affiliation(s)
- Leila B Giron
- The Wistar Institute, Philadelphia, PA, United States
| | - Harsh Dweep
- The Wistar Institute, Philadelphia, PA, United States
| | - Xiangfan Yin
- The Wistar Institute, Philadelphia, PA, United States
| | - Han Wang
- The Wistar Institute, Philadelphia, PA, United States
| | | | | | - Nicole Gorman
- The Wistar Institute, Philadelphia, PA, United States
| | - Clovis S Palmer
- The Burnet Institute, Melbourne, VIC, Australia.,Department of Infectious Diseases, Monash University, Melbourne, VIC, Australia
| | - Hsin-Yao Tang
- The Wistar Institute, Philadelphia, PA, United States
| | - Maliha W Shaikh
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States
| | - Christopher B Forsyth
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States.,Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Robert A Balk
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Netanel F Zilberstein
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Qin Liu
- The Wistar Institute, Philadelphia, PA, United States
| | | | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University, Chicago, IL, United States.,Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Alan Landay
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
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19
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Erturk-Hasdemir D, Ochoa-Repáraz J, Kasper DL, Kasper LH. Exploring the Gut-Brain Axis for the Control of CNS Inflammatory Demyelination: Immunomodulation by Bacteroides fragilis' Polysaccharide A. Front Immunol 2021; 12:662807. [PMID: 34025663 PMCID: PMC8131524 DOI: 10.3389/fimmu.2021.662807] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/16/2021] [Indexed: 12/12/2022] Open
Abstract
The symbiotic relationship between animals and their resident microorganisms has profound effects on host immunity. The human microbiota comprises bacteria that reside in the gastrointestinal tract and are involved in a range of inflammatory and autoimmune diseases. The gut microbiota's immunomodulatory effects extend to extraintestinal tissues, including the central nervous system (CNS). Specific symbiotic antigens responsible for inducing immunoregulation have been isolated from different bacterial species. Polysaccharide A (PSA) of Bacteroides fragilis is an archetypical molecule for host-microbiota interactions. Studies have shown that PSA has beneficial effects in experimental disease models, including experimental autoimmune encephalomyelitis (EAE), the most widely used animal model for multiple sclerosis (MS). Furthermore, in vitro stimulation with PSA promotes an immunomodulatory phenotype in human T cells isolated from healthy and MS donors. In this review, we discuss the current understanding of the interactions between gut microbiota and the host in the context of CNS inflammatory demyelination, the immunomodulatory roles of gut symbionts. More specifically, we also discuss the immunomodulatory effects of B. fragilis PSA in the gut-brain axis and its therapeutic potential in MS. Elucidation of the molecular mechanisms responsible for the microbiota's impact on host physiology offers tremendous promise for discovering new therapies.
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Affiliation(s)
| | | | - Dennis L. Kasper
- Department of Immunology, Harvard Medical School, Boston, MA, United States
| | - Lloyd H. Kasper
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth College, Hanover, NH, United States
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20
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The effects of diet and gut microbiota on the regulation of intestinal mucin glycosylation. Carbohydr Polym 2021; 258:117651. [DOI: 10.1016/j.carbpol.2021.117651] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 12/13/2022]
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21
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Liu H, Shiver AL, Price MN, Carlson HK, Trotter VV, Chen Y, Escalante V, Ray J, Hern KE, Petzold CJ, Turnbaugh PJ, Huang KC, Arkin AP, Deutschbauer AM. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Cell Rep 2021; 34:108789. [PMID: 33657378 PMCID: PMC8121099 DOI: 10.1016/j.celrep.2021.108789] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 11/30/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Harnessing the microbiota for beneficial outcomes is limited by our poor understanding of the constituent bacteria, as the functions of most of their genes are unknown. Here, we measure the growth of a barcoded transposon mutant library of the gut commensal Bacteroides thetaiotaomicron on 48 carbon sources, in the presence of 56 stress-inducing compounds, and during mono-colonization of gnotobiotic mice. We identify 516 genes with a specific phenotype under only one or a few conditions, enabling informed predictions of gene function. For example, we identify a glycoside hydrolase important for growth on type I rhamnogalacturonan, a DUF4861 protein for glycosaminoglycan utilization, a 3-keto-glucoside hydrolase for disaccharide utilization, and a tripartite multidrug resistance system specifically for bile salt tolerance. Furthermore, we show that B. thetaiotaomicron uses alternative enzymes for synthesizing nitrogen-containing metabolic precursors based on ammonium availability and that these enzymes are used differentially in vivo in a diet-dependent manner.
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Affiliation(s)
- Hualan Liu
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Anthony L Shiver
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Morgan N Price
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Hans K Carlson
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Valentine V Trotter
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Veronica Escalante
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jayashree Ray
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Kelsey E Hern
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Adam P Arkin
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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22
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Dudek M, Dieudonné A, Jouanneau D, Rochat T, Michel G, Sarels B, Thomas F. Regulation of alginate catabolism involves a GntR family repressor in the marine flavobacterium Zobellia galactanivorans DsijT. Nucleic Acids Res 2020; 48:7786-7800. [PMID: 32585009 PMCID: PMC7641319 DOI: 10.1093/nar/gkaa533] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/02/2020] [Accepted: 06/10/2020] [Indexed: 12/19/2022] Open
Abstract
Marine flavobacteria possess dedicated Polysaccharide Utilization Loci (PULs) enabling efficient degradation of a variety of algal polysaccharides. The expression of these PULs is tightly controlled by the presence of the substrate, yet details on the regulatory mechanisms are still lacking. The marine flavobacterium Zobellia galactanivorans DsijT digests many algal polysaccharides, including alginate from brown algae. Its complex Alginate Utilization System (AUS) comprises a PUL and several other loci. Here, we showed that the expression of the AUS is strongly and rapidly (<30 min) induced upon addition of alginate, leading to biphasic substrate utilization. Polymeric alginate is first degraded into smaller oligosaccharides that accumulate in the extracellular medium before being assimilated. We found that AusR, a GntR family protein encoded within the PUL, regulates alginate catabolism by repressing the transcription of most AUS genes. Based on our genetic, genomic, transcriptomic and biochemical results, we propose the first model of regulation for a PUL in marine bacteria. AusR binds to promoters of AUS genes via single, double or triple copies of operator. Upon addition of alginate, secreted enzymes expressed at a basal level catalyze the initial breakdown of the polymer. Metabolic intermediates produced during degradation act as effectors of AusR and inhibit the formation of AusR/DNA complexes, thus lifting transcriptional repression.
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Affiliation(s)
- Magda Dudek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anissa Dieudonné
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Diane Jouanneau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Tatiana Rochat
- Université Paris-Saclay, INRAE, UVSQ, VIM, 78350, Jouy-en-Josas, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Benoit Sarels
- Sorbonne Université, CNRS, Laboratoire Jacques-Louis Lions, Université de Paris, 75252 Paris, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
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23
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Arnolds KL, Martin CG, Lozupone CA. Blood type and the microbiome- untangling a complex relationship with lessons from pathogens. Curr Opin Microbiol 2020; 56:59-66. [PMID: 32663769 PMCID: PMC10104170 DOI: 10.1016/j.mib.2020.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/12/2022]
Abstract
The complex communities of microbes that constitute the human microbiome are influenced by host and environmental factors. Here, we address how a fundamental aspect of human biology, blood type, contributes to shaping this microscopic ecosystem. Although this question remains largely unexplored, we glean insights from decades of work describing relationships between pathogens and blood type. The bacterial strategies, molecular mechanisms, and host responses that shaped those relationships may parallel those that characterize how blood type and commensals interact. Understanding these nuanced interactions will expand our capacity to analyze and manipulate the human microbiome.
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Affiliation(s)
- Kathleen L Arnolds
- Department of Immunology and Microbiology, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Casey G Martin
- Department of Immunology and Microbiology, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Catherine A Lozupone
- Department of Medicine, Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver Anschutz Medical Campus, Aurora, CO 80045, USA.
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24
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Lactoferrin and lactoferricin B reduce adhesion and biofilm formation in the intestinal symbionts Bacteroides fragilis and Bacteroides thetaiotaomicron. Anaerobe 2020; 64:102232. [DOI: 10.1016/j.anaerobe.2020.102232] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 01/01/2023]
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25
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The uroS and yifB Genes Conserved among Tetrapyrrole Synthesizing-Deficient Bacteroidales Are Involved in Bacteroides fragilis Heme Assimilation and Survival in Experimental Intra-abdominal Infection and Intestinal Colonization. Infect Immun 2020; 88:IAI.00103-20. [PMID: 32457103 DOI: 10.1128/iai.00103-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/15/2020] [Indexed: 01/01/2023] Open
Abstract
The human intestinal anaerobic commensal and opportunistic pathogen Bacteroides fragilis does not synthesize the tetrapyrrole protoporphyrin IX in order to form heme that is required for growth stimulation and survival in vivo Consequently, B. fragilis acquires essential heme from host tissues during extraintestinal infection. The absence of several genes necessary for de novo heme biosynthesis is a common characteristic of many anaerobic bacteria; however, the uroS gene, encoding a uroporphyrinogen III synthase for an early step of heme biosynthesis, is conserved among the heme-requiring Bacteroidales that inhabit the mammalian gastrointestinal tract. In this study, we show that the ability of B. fragilis to utilize heme or protoporphyrin IX for growth was greatly reduced in a ΔuroS mutant. This growth defect appears to be linked to the suppression of reverse chelatase and ferrochelatase activities in the absence of uroS In addition, this ΔuroS suppressive effect was enhanced by the deletion of the yifB gene, which encodes an Mg2+-chelatase protein belonging to the ATPases associated with various cellular activities (AAA+) superfamily of proteins. Furthermore, the ΔuroS mutant and the ΔuroS ΔyifB double mutant had a severe survival defect compared to the parent strain in competitive infection assays using animal models of intra-abdominal infection and intestinal colonization. This shows that the presence of the uroS and yifB genes in B. fragilis seems to be linked to pathophysiological and nutritional competitive fitness for survival in host tissues. Genetic complementation studies and enzyme kinetics assays indicate that B. fragilis UroS is functionally different from canonical bacterial UroS proteins. Taken together, these findings show that heme assimilation and metabolism in the anaerobe B. fragilis have diverged from those of aerobic and facultative anaerobic pathogenic bacteria.
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26
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Chen P, Liu R, Huang M, Zhu J, Wei D, Castellino FJ, Dang G, Xie F, Li G, Cui Z, Liu S, Zhang Y. A unique combination of glycoside hydrolases in Streptococcus suis specifically and sequentially acts on host-derived αGal-epitope glycans. J Biol Chem 2020; 295:10638-10652. [PMID: 32518157 DOI: 10.1074/jbc.ra119.011977] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 06/06/2020] [Indexed: 01/02/2023] Open
Abstract
Infections by many bacterial pathogens rely on their ability to degrade host glycans by producing glycoside hydrolases (GHs). Here, we discovered a conserved multifunctional GH, SsGalNagA, containing a unique combination of two family 32 carbohydrate-binding modules (CBM), a GH16 domain and a GH20 domain, in the zoonotic pathogen Streptococcus suis 05ZYH33. Enzymatic assays revealed that the SsCBM-GH16 domain displays endo-(β1,4)-galactosidase activity specifically toward the host-derived αGal epitope Gal(α1,3)Gal(β1,4)Glc(NAc)-R, whereas the SsGH20 domain has a wide spectrum of exo-β-N-acetylhexosaminidase activities, including exo-(β1,3)-N-acetylglucosaminidase activity, and employs this activity to act in tandem with SsCBM-GH16 on the αGal-epitope glycan. Further, we found that the CBM32 domain adjacent to the SsGH16 domain is indispensable for SsGH16 catalytic activity. Surface plasmon resonance experiments uncovered that both CBM32 domains specifically bind to αGal-epitope glycan, and together they had a KD of 3.5 mm toward a pentasaccharide αGal-epitope glycan. Cell-binding and αGal epitope removal assays revealed that SsGalNagA efficiently binds to both swine erythrocytes and tracheal epithelial cells and removes the αGal epitope from these cells, suggesting that SsGalNagA functions in nutrient acquisition or alters host signaling in S. suis Both binding and removal activities were blocked by an αGal-epitope glycan. SsGalNagA is the first enzyme reported to sequentially act on a glycan containing the αGal epitope. These findings shed detailed light on the evolution of GHs and an important host-pathogen interaction.
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Affiliation(s)
- Ping Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ran Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Mengmeng Huang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinlu Zhu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Dong Wei
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Francis J Castellino
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA.,W. M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, Indiana, USA
| | - Guanghui Dang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Fang Xie
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Gang Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ziyin Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yueling Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Ma J, Zhang Z, Pan Z, Bai Q, Zhong X, Zhu Y, Zhang Y, Wu Z, Liu G, Yao H. Streptococcus suis Uptakes Carbohydrate Source from Host Glycoproteins by N-glycans Degradation System for Optimal Survival and Full Virulence during Infection. Pathogens 2020; 9:E387. [PMID: 32443590 PMCID: PMC7281376 DOI: 10.3390/pathogens9050387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 02/07/2023] Open
Abstract
Infection with the epidemic virulent strain of Streptococcus suis serotype 2 (SS2) can cause septicemia in swine and humans, leading to pneumonia, meningitis and even cytokine storm of Streptococcal toxic shock-like syndrome. Despite some progress concerning the contribution of bacterial adhesion, biofilm, toxicity and stress response to the SS2 systemic infection, the precise mechanism underlying bacterial survival and growth within the host bloodstream remains elusive. Here, we reported the SS2 virulent strains with a more than 20 kb endoSS-related insertion region that showed significantly higher proliferative ability in swine serum than low-virulent strains. Further study identified a complete N-glycans degradation system encoded within this insertion region, and found that both GH92 and EndoSS contribute to bacterial virulence, but that only DndoSS was required for optimal growth of SS2 in host serum. The supplement of hydrolyzed high-mannose-containing glycoprotein by GH92 and EndoSS could completely restore the growth deficiency of endoSS deletion mutant in swine serum. EndoSS only hydrolyzed a part of the model glycoprotein RNase B with high-mannose N-linked glycoforms into a low molecular weight form, and the solo activity of GH92 could not show any changes comparing with the blank control in SDS-PAGE gel. However, complete hydrolyzation was observed under the co-incubation of EndoSS and GH92, suggesting GH92 may degrade the high-mannose arms of N-glycans to generate a substrate for EndoSS. In summary, these findings provide compelling evidences that EndoSS-related N-glycans degradation system may enable SS2 to adapt to host serum-specific availability of carbon sources from glycoforms, and be required for optimal colonization and full virulence during systemic infection.
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Affiliation(s)
- Jiale Ma
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Ze Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Zihao Pan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Qiankun Bai
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Xiaojun Zhong
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Yinchu Zhu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Yue Zhang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Zongfu Wu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Guangjin Liu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
| | - Huochun Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (Z.Z.); (Z.P.); (Q.B.); (X.Z.); (Y.Z.); (Y.Z.); (Z.W.); (G.L.)
- Key Lab of Animal Bacteriology, Ministry of Agriculture, Nanjing 210095, China
- OIE Reference Lab for Swine Streptococcosis, Nanjing 210095, China
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Spatially distinct physiology of Bacteroides fragilis within the proximal colon of gnotobiotic mice. Nat Microbiol 2020; 5:746-756. [PMID: 32152589 PMCID: PMC7426998 DOI: 10.1038/s41564-020-0683-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 02/03/2020] [Indexed: 12/11/2022]
Abstract
A complex microbiota inhabits various microenvironments of the gut, with some symbiotic bacteria having evolved traits to invade the epithelial mucus layer and reside deep within intestinal tissue of animals. Whether these distinct bacterial communities across gut biogeographies exhibit divergent behaviors remains largely unknown. Global transcriptomic analysis to investigate microbial physiology in specific mucosal niches has been hampered technically by overabundance of host RNA. Herein, we employed hybrid selection RNA sequencing (hsRNA-Seq) to enable detailed spatial transcriptomic profiling of a prominent human commensal as it colonizes the colonic lumen, mucus or epithelial tissue of mice. Compared to conventional RNA-Seq, hsRNA-Seq increased reads mapping to the Bacteroides fragilis genome by 48- and 154-fold in mucus and tissue, respectively, allowing for high fidelity comparisons across biogeographic sites. Near the epithelium, B. fragilis up-regulated numerous genes involved in protein synthesis, indicating that bacteria inhabiting the mucosal niche are metabolically active. Further, a specific sulfatase (BF3086) and glycosyl hydrolase (BF3134) were highly induced in mucus and tissue compared to bacteria in the lumen. In-frame deletion of these genes impaired in vitro growth on mucus as a carbon source, as well as mucosal colonization of mice. Mutants in either B. fragilis gene displayed a fitness defect in competing for colonization against bacterial challenge, revealing the importance of site-specific gene expression for robust host-microbial symbiosis. As a versatile tool, hsRNA-Seq can be deployed to explore the in vivo spatial physiology of numerous bacterial pathogens or commensals.
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The gastrointestinal pathogen Campylobacter jejuni metabolizes sugars with potential help from commensal Bacteroides vulgatus. Commun Biol 2020; 3:2. [PMID: 31925306 PMCID: PMC6946681 DOI: 10.1038/s42003-019-0727-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 12/04/2019] [Indexed: 01/07/2023] Open
Abstract
Although the gastrointestinal pathogen Campylobacter jejuni was considered asaccharolytic, >50% of sequenced isolates possess an operon for L-fucose utilization. In C. jejuni NCTC11168, this pathway confers L-fucose chemotaxis and competitive colonization advantages in the piglet diarrhea model, but the catabolic steps remain unknown. Here we solved the putative dehydrogenase structure, resembling FabG of Burkholderia multivorans. The C. jejuni enzyme, FucX, reduces L-fucose and D-arabinose in vitro and both sugars are catabolized by fuc-operon encoded enzymes. This enzyme alone confers chemotaxis to both sugars in a non-carbohydrate-utilizing C. jejuni strain. Although C. jejuni lacks fucosidases, the organism exhibits enhanced growth in vitro when co-cultured with Bacteroides vulgatus, suggesting scavenging may occur. Yet, when excess amino acids are available, C. jejuni prefers them to carbohydrates, indicating a metabolic hierarchy exists. Overall this study increases understanding of nutrient metabolism by this pathogen, and identifies interactions with other gut microbes.
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30
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Pabst O, Slack E. IgA and the intestinal microbiota: the importance of being specific. Mucosal Immunol 2020; 13:12-21. [PMID: 31740744 PMCID: PMC6914667 DOI: 10.1038/s41385-019-0227-4] [Citation(s) in RCA: 301] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/27/2019] [Accepted: 09/28/2019] [Indexed: 02/04/2023]
Abstract
Secretory IgA has long been a divisive molecule. Some immunologists point to the mild phenotype of IgA deficiency to justify ignoring it, while some consider its abundance and evolutionary history as grounds for its importance. Further, there is extensive and growing disagreement over the relative importance of affinity-matured, T cell-dependent IgA vs. "natural" and T cell-independent IgA in both microbiota and infection control. As with all good arguments, there is good data supporting different opinions. Here we revisit longstanding questions in IgA biology. We start the discussion from the question of intestinal IgA antigen specificity and critical definitions regarding IgA induction, specificity, and function. These definitions must then be tessellated with the cellular and molecular pathways shaping IgA responses, and the mechanisms by which IgA functions. On this basis we propose how IgA may contribute to the establishment and maintenance of beneficial interactions with the microbiota.
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Affiliation(s)
- Oliver Pabst
- 0000 0001 0728 696Xgrid.1957.aInstitute of Molecular Medicine, RWTH Aachen University, Aachen, Germany
| | - Emma Slack
- 0000 0001 2156 2780grid.5801.cInstitute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
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Larsbrink J, McKee LS. Bacteroidetes bacteria in the soil: Glycan acquisition, enzyme secretion, and gliding motility. ADVANCES IN APPLIED MICROBIOLOGY 2020; 110:63-98. [PMID: 32386606 DOI: 10.1016/bs.aambs.2019.11.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The secretion of extracellular enzymes by soil microbes is rate-limiting in the recycling of biomass. Fungi and bacteria compete and collaborate for nutrients in the soil, with wide ranging ecological impacts. Within soil microbiota, the Bacteroidetes tend to be a dominant phylum, just like in human and animal intestines. The Bacteroidetes thrive because of their ability to secrete diverse arrays of carbohydrate-active enzymes (CAZymes) that target the highly varied glycans in the soil. Bacteroidetes use an energy-saving system of genomic organization, whereby most of their CAZymes are grouped into Polysaccharide Utilization Loci (PULs). These loci enable high level production of specific CAZymes only when their substrate glycans are abundant in the local environment. This gives the Bacteroidetes a clear advantage over other species in the competitive soil environment, further enhanced by the phylum-specific Type IX Secretion System (T9SS). The T9SS is highly effective at secreting CAZymes and/or tethering them to the cell surface, and is tightly coupled to the ability to rapidly glide over solid surfaces, a connection that promotes an active hunt for nutrition. Although the soil Bacteroidetes are less well studied than human gut symbionts, research is uncovering important biochemical and physiological phenomena. In this review, we summarize the state of the art on research into the CAZymes secreted by soil Bacteroidetes in the contexts of microbial soil ecology and the discovery of novel CAZymes for use in industrial biotechnology. We hope that this review will stimulate further investigations into the somewhat neglected enzymology of non-gut Bacteroidetes.
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Affiliation(s)
- Johan Larsbrink
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lauren Sara McKee
- Wallenberg Wood Science Center, Gothenburg and Stockholm, Sweden; Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, Sweden.
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32
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Valguarnera E, Wardenburg JB. Good Gone Bad: One Toxin Away From Disease for Bacteroides fragilis. J Mol Biol 2019; 432:765-785. [PMID: 31857085 DOI: 10.1016/j.jmb.2019.12.003] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 11/27/2019] [Accepted: 12/05/2019] [Indexed: 02/06/2023]
Abstract
The human gut is colonized by hundreds of trillions of microorganisms whose acquisition begins during early infancy. Species from the Bacteroides genus are ubiquitous commensals, comprising about thirty percent of the human gut microbiota. Bacteroides fragilis is one of the least abundant Bacteroides species, yet is the most common anaerobe isolated from extraintestinal infections in humans. A subset of B. fragilis strains carry a genetic element that encodes a metalloprotease enterotoxin named Bacteroides fragilis toxin, or BFT. Toxin-bearing strains, or Enterotoxigenic B. fragilis (ETBF) cause acute and chronic intestinal disease in children and adults. Despite this association with disease, around twenty percent of the human population appear to be asymptomatic carriers of ETBF. BFT damages the colonic epithelial barrier by inducing cleavage of the zonula adherens protein E-cadherin and initiating a cell signaling response characterized by inflammation and c-Myc-dependent pro-oncogenic hyperproliferation. As a consequence, mice harboring genetic mutations that predispose to colonic inflammation or tumor formation are uniquely susceptible to toxin-mediated injury. The recent observation of ETBF-bearing biofilms in colon biopsies from humans with colon cancer susceptibility loci strongly suggests that ETBF is a driver of colorectal cancer. This article will address ETBF biology from a host-pathobiont perspective, including clinical data, analysis of molecular mechanisms of disease, and the complex ecological context of the human gut.
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Affiliation(s)
- Ezequiel Valguarnera
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave. Box 8208, St. Louis, MO 63110
| | - Juliane Bubeck Wardenburg
- Department of Pediatrics, Washington University School of Medicine, 660 S. Euclid Ave. Box 8208, St. Louis, MO 63110.
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33
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Monaghan TM, Pučić-Baković M, Vučković F, Lee C, Kao D. Decreased Complexity of Serum N-glycan Structures Associates with Successful Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection. Gastroenterology 2019; 157:1676-1678.e3. [PMID: 31476300 DOI: 10.1053/j.gastro.2019.08.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 12/02/2022]
Affiliation(s)
- Tanya M Monaghan
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK; Nottingham Digestive Diseases Centre, School of Medicine, University of Nottingham, Nottingham, UK.
| | | | | | - Christine Lee
- Vancouver Island Health Authority, Victoria, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dina Kao
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
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Briliūtė J, Urbanowicz PA, Luis AS, Baslé A, Paterson N, Rebello O, Hendel J, Ndeh DA, Lowe EC, Martens EC, Spencer DIR, Bolam DN, Crouch LI. Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci. Nat Microbiol 2019; 4:1571-1581. [PMID: 31160824 PMCID: PMC7617214 DOI: 10.1038/s41564-019-0466-x] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/24/2019] [Indexed: 02/08/2023]
Abstract
Glycans are the major carbon sources available to the human colonic microbiota. Numerous N-glycosylated proteins are found in the human gut, from both dietary and host sources, including immunoglobulins such as IgA that are secreted into the intestine at high levels. Here, we show that many mutualistic gut Bacteroides spp. have the capacity to utilize complex N-glycans (CNGs) as nutrients, including those from immunoglobulins. Detailed mechanistic studies using transcriptomic, biochemical, structural and genetic techniques reveal the pathway employed by Bacteroides thetaiotaomicron (Bt) for CNG degradation. The breakdown process involves an extensive enzymatic apparatus encoded by multiple non-adjacent loci and comprises 19 different carbohydrate-active enzymes from different families, including a CNG-specific endo-glycosidase activity. Furthermore, CNG degradation involves the activity of carbohydrate-active enzymes that have previously been implicated in the degradation of other classes of glycan. This complex and diverse apparatus provides Bt with the capacity to access the myriad different structural variants of CNGs likely to be found in the intestinal niche.
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Affiliation(s)
- Justina Briliūtė
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | | | - Ana S Luis
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | | | - Didier A Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.
| | - Lucy I Crouch
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.
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Lu Z, Imlay JA. A conserved motif liganding the [4Fe-4S] cluster in [4Fe-4S] fumarases prevents irreversible inactivation of the enzyme during hydrogen peroxide stress. Redox Biol 2019; 26:101296. [PMID: 31465957 PMCID: PMC6831887 DOI: 10.1016/j.redox.2019.101296] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 08/04/2019] [Accepted: 08/07/2019] [Indexed: 11/16/2022] Open
Abstract
Organisms have evolved two different classes of the ubiquitous enzyme fumarase: the [4Fe–4S] cluster-containing class I enzymes are oxidant-sensitive, whereas the class II enzymes are iron-free and therefore oxidant-resistant. When hydrogen peroxide (H2O2) attacks the most-studied [4Fe–4S] fumarases, only the cluster is damaged, and thus the cell can rapidly repair the enzyme. However, this study shows that when elevated levels of H2O2 oxidized the class I fumarase of the obligate anaerobe Bacteroides thetaiotaomicron (Bt-Fum), a hydroxyl-like radical species was produced that caused irreversible covalent damage to the polypeptide. Unlike the fumarase of oxygen-tolerant bacteria, Bt-Fum lacks a key cysteine residue in the typical “CXnCX2C″ motif that ligands [4Fe–4S] clusters. Consequently H2O2 can access and oxidize an iron atom other than the catalytic one in its cluster. Phylogenetic analysis showed that certain clades of bacteria may have evolved the full “CXnCX2C″ motif to shield the [4Fe–4S] cluster of fumarase. This effect was reproduced by the construction of a chimeric enzyme. These data demonstrate the irreversible oxidation of Fe–S cluster enzymes and may recapitulate evolutionary steps that occurred when microorganisms originally confronted oxidizing environments. It is also suggested that, if H2O2 is generated within the colon as a consequence of inflammation or the action of lactic acid bacteria, the inactivation of fumarase could potentially impair the central fermentation pathway of Bacteroides species and contribute to gut dysbiosis.
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Affiliation(s)
- Zheng Lu
- Department of Biology, Guangdong Provincial Key Laboratory of Marine Biotechnology, STU-UNIVPM Joint Algal Research Center, Shantou University, Shantou, 515063, China.
| | - James A Imlay
- Department of Microbiology, University of Illinois, 601 S. Goodwin Ave., Urbana, IL, 61801, USA
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Terrapon N, Lombard V, Drula É, Lapébie P, Al-Masaudi S, Gilbert HJ, Henrissat B. PULDB: the expanded database of Polysaccharide Utilization Loci. Nucleic Acids Res 2019; 46:D677-D683. [PMID: 29088389 PMCID: PMC5753385 DOI: 10.1093/nar/gkx1022] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 10/25/2017] [Indexed: 12/12/2022] Open
Abstract
The Polysaccharide Utilization Loci (PUL) database was launched in 2015 to present PUL predictions in ∼70 Bacteroidetes species isolated from the human gastrointestinal tract, as well as PULs derived from the experimental data reported in the literature. In 2018 PULDB offers access to 820 genomes, sampled from various environments and covering a much wider taxonomical range. A Krona dynamic chart was set up to facilitate browsing through taxonomy. Literature surveys now allows the presentation of the most recent (i) PUL repertoires deduced from RNAseq large-scale experiments, (ii) PULs that have been subjected to in-depth biochemical analysis and (iii) new Carbohydrate-Active enzyme (CAZyme) families that contributed to the refinement of PUL predictions. To improve PUL visualization and genome browsing, the previous annotation of genes encoding CAZymes, regulators, integrases and SusCD has now been expanded to include functionally relevant protein families whose genes are significantly found in the vicinity of PULs: sulfatases, proteases, ROK repressors, epimerases and ATP-Binding Cassette and Major Facilitator Superfamily transporters. To cope with cases where susCD may be absent due to incomplete assemblies/split PULs, we present ‘CAZyme cluster’ predictions. Finally, a PUL alignment tool, operating on the tagged families instead of amino-acid sequences, was integrated to retrieve PULs similar to a query of interest. The updated PULDB website is accessible at www.cazy.org/PULDB_new/
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Affiliation(s)
- Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Élodie Drula
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Pascal Lapébie
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France
| | - Saad Al-Masaudi
- Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, F-13288 Marseille, France.,USC1408 Architecture et Fonction des Macromolécules Biologiques, Institut National de la Recherche Agronomique, F-13288 Marseille, France.,Department of Biological Sciences, King Abdulaziz University, 23218 Jeddah, Saudi Arabia
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Wang M, Zhu J, Lubman DM, Gao C. Aberrant glycosylation and cancer biomarker discovery: a promising and thorny journey. Clin Chem Lab Med 2019; 57:407-416. [PMID: 30138110 PMCID: PMC6785348 DOI: 10.1515/cclm-2018-0379] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Accepted: 07/15/2018] [Indexed: 12/12/2022]
Abstract
Glycosylation is among the most important post-translational modifications for proteins and is of intrinsic complex character compared with DNAs and naked proteins. Indeed, over 50%-70% of proteins in circulation are glycosylated, and the "sweet attachments" have versatile structural and functional implications. Both the configuration and composition of the attached glycans affect the biological activities of consensus proteins significantly. Glycosylation is generated by complex biosynthetic pathways comprising hundreds of glycosyltransferases, glycosidases, transcriptional factors, transporters and the protein backbone. In addition, lack of direct genetic templates and glyco-specific antibodies such as those commonly used in DNA amplification and protein capture makes research on glycans and glycoproteins even more difficult, thus resulting in sparse knowledge on the pathophysiological implications of glycosylation. Fortunately, cutting-edge technologies have afforded new opportunities and approaches for investigating cancer-related glycosylation. Thus, glycans as well as aberrantly glycosylated protein-based cancer biomarkers have been increasingly recognized. This mini-review highlights the most recent developments in glyco-biomarker studies in an effort to discover clinically relevant cancer biomarkers using advanced analytical methodologies such as mass spectrometry, high-performance liquid chromatographic/ultra-performance liquid chromatography, capillary electrophoresis, and lectin-based technologies. Recent clinical-centered glycobiological studies focused on determining the regulatory mechanisms and the relation with diagnostics, prognostics and even therapeutics are also summarized. These studies indicate that glycomics is a treasure waiting to be mined where the growth of cancer-related glycomics and glycoproteomics is the next great challenge after genomics and proteomics.
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Affiliation(s)
- Mengmeng Wang
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai, P.R. China
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David M. Lubman
- Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Chunfang Gao
- Department of Laboratory Medicine, Shanghai Eastern Hepatobiliary Surgery Hospital, Shanghai 200438, P.R. China
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Bhat AH, Maity S, Giri K, Ambatipudi K. Protein glycosylation: Sweet or bitter for bacterial pathogens? Crit Rev Microbiol 2019; 45:82-102. [PMID: 30632429 DOI: 10.1080/1040841x.2018.1547681] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Protein glycosylation systems in many bacteria are often associated with crucial biological processes like pathogenicity, immune evasion and host-pathogen interactions, implying the significance of protein-glycan linkage. Similarly, host protein glycosylation has been implicated in antimicrobial activity as well as in promoting growth of beneficial strains. In fact, few pathogens notably modulate host glycosylation machineries to facilitate their survival. To date, diverse chemical and biological strategies have been developed for conjugate vaccine production for disease control. Bioconjugate vaccines, largely being produced by glycoengineering using PglB (the N-oligosaccharyltransferase from Campylobacter jejuni) in suitable bacterial hosts, have been highly promising with respect to their effectiveness in providing protective immunity and ease of production. Recently, a novel method of glycoconjugate vaccine production involving an O-oligosaccharyltransferase, PglL from Neisseria meningitidis, has been optimized. Nevertheless, many questions on defining antigenic determinants, glycosylation markers, species-specific differences in glycosylation machineries, etc. still remain unanswered, necessitating further exploration of the glycosylation systems of important pathogens. Hence, in this review, we will discuss the impact of bacterial protein glycosylation on its pathogenesis and the interaction of pathogens with host protein glycosylation, followed by a discussion on strategies used for bioconjugate vaccine development.
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Affiliation(s)
- Aadil Hussain Bhat
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
| | - Sudipa Maity
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
| | - Kuldeep Giri
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
| | - Kiran Ambatipudi
- a Department of Biotechnology , Indian Institute of Technology Roorkee , Roorkee , Uttarakhand 247667 , India
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Mu C, Cai Z, Bian G, Du Y, Ma S, Su Y, Liu L, Voglmeir J, Huang R, Zhu W. New Insights into Porcine Milk N-Glycome and the Potential Relation with Offspring Gut Microbiome. J Proteome Res 2018; 18:1114-1124. [DOI: 10.1021/acs.jproteome.8b00789] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Reichenbach T, Kalyani D, Gandini R, Svartström O, Aspeborg H, Divne C. Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins. PLoS One 2018; 13:e0204703. [PMID: 30261037 PMCID: PMC6160142 DOI: 10.1371/journal.pone.0204703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/12/2018] [Indexed: 12/25/2022] Open
Abstract
Commensal and pathogenic bacteria have evolved efficient enzymatic pathways to feed on host carbohydrates, including protein-linked glycans. Most proteins of the human innate and adaptive immune system are glycoproteins where the glycan is critical for structural and functional integrity. Besides enabling nutrition, the degradation of host N-glycans serves as a means for bacteria to modulate the host's immune system by for instance removing N-glycans on immunoglobulin G. The commensal bacterium Cutibacterium acnes is a gram-positive natural bacterial species of the human skin microbiota. Under certain circumstances, C. acnes can cause pathogenic conditions, acne vulgaris, which typically affects 80% of adolescents, and can become critical for immunosuppressed transplant patients. Others have shown that C. acnes can degrade certain host O-glycans, however, no degradation pathway for host N-glycans has been proposed. To investigate this, we scanned the C. acnes genome and were able to identify a set of gene candidates consistent with a cytoplasmic N-glycan-degradation pathway of the canonical eukaryotic N-glycan core. We also found additional gene sequences containing secretion signals that are possible candidates for initial trimming on the extracellular side. Furthermore, one of the identified gene products of the cytoplasmic pathway, AEE72695, was produced and characterized, and found to be a functional, dimeric exo-β-1,4-mannosidase with activity on the β-1,4 glycosidic bond between the second N-acetylglucosamine and the first mannose residue in the canonical eukaryotic N-glycan core. These findings corroborate our model of the cytoplasmic part of a C. acnes N-glycan degradation pathway.
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Affiliation(s)
- Tom Reichenbach
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dayanand Kalyani
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rosaria Gandini
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Olov Svartström
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Henrik Aspeborg
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
| | - Christina Divne
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology, and Health (CBH), KTH Royal Institute of Technology, Stockholm, Sweden
- * E-mail:
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2013-2014. MASS SPECTROMETRY REVIEWS 2018; 37:353-491. [PMID: 29687922 DOI: 10.1002/mas.21530] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/29/2016] [Indexed: 06/08/2023]
Abstract
This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.
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Affiliation(s)
- David J Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, United Kingdom
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Hobbs JK, Pluvinage B, Boraston AB. Glycan-metabolizing enzymes in microbe-host interactions: the Streptococcus pneumoniae paradigm. FEBS Lett 2018; 592:3865-3897. [PMID: 29608212 DOI: 10.1002/1873-3468.13045] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 12/31/2022]
Abstract
Streptococcus pneumoniae is a frequent colonizer of the upper airways; however, it is also an accomplished pathogen capable of causing life-threatening diseases. To colonize and cause invasive disease, this bacterium relies on a complex array of factors to mediate the host-bacterium interaction. The respiratory tract is rich in functionally important glycoconjugates that display a vast range of glycans, and, thus, a key component of the pneumococcus-host interaction involves an arsenal of bacterial carbohydrate-active enzymes to depolymerize these glycans and carbohydrate transporters to import the products. Through the destruction of host glycans, the glycan-specific metabolic machinery deployed by S. pneumoniae plays a variety of roles in the host-pathogen interaction. Here, we review the processing and metabolism of the major host-derived glycans, including N- and O-linked glycans, Lewis and blood group antigens, proteoglycans, and glycogen, as well as some dietary glycans. We discuss the role of these metabolic pathways in the S. pneumoniae-host interaction, speculate on the potential of key enzymes within these pathways as therapeutic targets, and relate S. pneumoniae as a model system to glycan processing in other microbial pathogens.
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Affiliation(s)
- Joanne K Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, British Columbia, Canada
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Erturk-Hasdemir D, Kasper DL. Finding a needle in a haystack: Bacteroides fragilis polysaccharide A as the archetypical symbiosis factor. Ann N Y Acad Sci 2018. [PMID: 29528123 DOI: 10.1111/nyas.13660] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Starting from birth, all animals develop a symbiotic relationship with their resident microorganisms that benefits both the microbe and the host. Recent advances in technology have substantially improved our ability to direct research toward the identification of important microbial species that affect host physiology. The identification of specific commensal molecules from these microbes and their mechanisms of action is still in its early stages. Polysaccharide A (PSA) of Bacteroides fragilis is the archetypical example of a commensal molecule that can modulate the host immune system in health and disease. This zwitterionic polysaccharide has a critical impact on the development of the mammalian immune system and also on the stimulation of interleukin 10-producing CD4+ T cells; consequently, PSA confers benefits to the host with regard to experimental autoimmune, inflammatory, and infectious diseases. In this review, we summarize the current understanding of the immunomodulatory effects of B. fragilis PSA and discuss these effects as a novel immunological paradigm. In particular, we discuss recent advances in our understanding of the unique functional mechanisms of this molecule and its therapeutic potential, and we review the recent literature in the field of microbiome research aimed at discovering new commensal products and their immunomodulatory potential.
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Affiliation(s)
- Deniz Erturk-Hasdemir
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
| | - Dennis L Kasper
- Division of Immunology, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
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Yoshida S, Mitani H, Kamata M, Ohtsuka A, Otomaru K, Obi T, Kanouchi H. Effect of dietary fermented mushroom bed on egg production in laying hens. Biosci Biotechnol Biochem 2017; 81:2204-2208. [PMID: 29144889 DOI: 10.1080/09168451.2017.1383846] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Egg productivity is declined by stress. It has been reported that some food supplements can improve the egg productivity due to a reduction of environmental stress. We evaluated the effect of fermented waste mushroom bed (FWMB) as a dietary additive on egg productivity. Hens were fed control food (control group, n = 100) or 3% FWMB-added food (FWMB group, n = 100) for 16 months. The number of eggs, soft-shelled eggs, and broken eggs were recorded for 15 months. We also evaluated stress-related markers (ovotransferrin, lipid peroxide, and the heterophil-to-lymphocyte ratio). The FWMB group had slightly increased egg production compared with control hens. The FWMB group produced significantly less broken and soft-shelled eggs than the control group. All stress-related markers were significantly lower in the FWMB group than in the control group. Gut flora was also affected by FWMB feeding. The increased egg production and decreased proportion of broken and soft-shelled eggs might be related to the prevention of stressful conditions by FWMB.
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Affiliation(s)
- Shu Yoshida
- a Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine , Kagoshima University , Kagoshima , Japan
| | - Hiroaki Mitani
- b Research & Development Division , Kamada Co. Ltd ., Kagoshima , Japan
| | - Masato Kamata
- b Research & Development Division , Kamada Co. Ltd ., Kagoshima , Japan
| | - Akira Ohtsuka
- c Department of Biochemical Science and Technology , Kagoshima University , Kagoshima , Japan
| | - Konosuke Otomaru
- d Laboratory of Veterinary Hospital, Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine , Kagoshima University , Kagoshima , Japan
| | - Takeshi Obi
- a Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine , Kagoshima University , Kagoshima , Japan
| | - Hiroaki Kanouchi
- e Laboratory of Veterinary Pathobiology, Department of Veterinary Medicine, Joint Faculty of Veterinary Medicine , Kagoshima University , Kagoshima , Japan
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Navigating the Gut Buffet: Control of Polysaccharide Utilization in Bacteroides spp. Trends Microbiol 2017; 25:1005-1015. [DOI: 10.1016/j.tim.2017.06.009] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/09/2017] [Accepted: 06/20/2017] [Indexed: 12/26/2022]
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Cartmell A, Lowe EC, Baslé A, Firbank SJ, Ndeh DA, Murray H, Terrapon N, Lombard V, Henrissat B, Turnbull JE, Czjzek M, Gilbert HJ, Bolam DN. How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Proc Natl Acad Sci U S A 2017; 114:7037-7042. [PMID: 28630303 PMCID: PMC5502631 DOI: 10.1073/pnas.1704367114] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human microbiota, which plays an important role in health and disease, uses complex carbohydrates as a major source of nutrients. Utilization hierarchy indicates that the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS) are high-priority carbohydrates for Bacteroides thetaiotaomicron, a prominent member of the human microbiota. The sulfation patterns of these glycosaminoglycans are highly variable, which presents a significant enzymatic challenge to the polysaccharide lyases and sulfatases that mediate degradation. It is possible that the bacterium recruits lyases with highly plastic specificities and expresses a repertoire of enzymes that target substructures of the glycosaminoglycans with variable sulfation or that the glycans are desulfated before cleavage by the lyases. To distinguish between these mechanisms, the components of the B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. The data showed that the bacterium expressed a single-surface endo-acting lyase that cleaved HS, reflecting its higher molecular weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, with each enzyme displaying specificity for substructures within these glycosaminoglycans that display a different degree of sulfation. Furthermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides, indicating that the model developed is of generic relevance to this important microbial community.
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Affiliation(s)
- Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Susan J Firbank
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Didier A Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Heath Murray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
- Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeremy E Turnbull
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Mirjam Czjzek
- Sorbonne Universités, Université Pierre-et-Marie-Curie, Université Paris 06, F-29688 Roscoff cedex, Bretagne, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff cedex, Bretagne, France
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;
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Wadsworth WD, Argiento R, Guindani M, Galloway-Pena J, Shelburne SA, Vannucci M. An integrative Bayesian Dirichlet-multinomial regression model for the analysis of taxonomic abundances in microbiome data. BMC Bioinformatics 2017; 18:94. [PMID: 28178947 PMCID: PMC5299727 DOI: 10.1186/s12859-017-1516-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 01/31/2017] [Indexed: 12/19/2022] Open
Abstract
Background The Human Microbiome has been variously associated with the immune-regulatory mechanisms involved in the prevention or development of many non-infectious human diseases such as autoimmunity, allergy and cancer. Integrative approaches which aim at associating the composition of the human microbiome with other available information, such as clinical covariates and environmental predictors, are paramount to develop a more complete understanding of the role of microbiome in disease development. Results In this manuscript, we propose a Bayesian Dirichlet-Multinomial regression model which uses spike-and-slab priors for the selection of significant associations between a set of available covariates and taxa from a microbiome abundance table. The approach allows straightforward incorporation of the covariates through a log-linear regression parametrization of the parameters of the Dirichlet-Multinomial likelihood. Inference is conducted through a Markov Chain Monte Carlo algorithm, and selection of the significant covariates is based upon the assessment of posterior probabilities of inclusions and the thresholding of the Bayesian false discovery rate. We design a simulation study to evaluate the performance of the proposed method, and then apply our model on a publicly available dataset obtained from the Human Microbiome Project which associates taxa abundances with KEGG orthology pathways. The method is implemented in specifically developed R code, which has been made publicly available. Conclusions Our method compares favorably in simulations to several recently proposed approaches for similarly structured data, in terms of increased accuracy and reduced false positive as well as false negative rates. In the application to the data from the Human Microbiome Project, a close evaluation of the biological significance of our findings confirms existing associations in the literature. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1516-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Raffaele Argiento
- ESOMAS Department, University of Torino and Collegio Carlo Alberto, Torino, Italy
| | - Michele Guindani
- Department of Statistics, University of California, Irvine, CA, USA
| | - Jessica Galloway-Pena
- Department of Infectious Disease, Infection Control, and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Samuel A Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, 77030, TX, USA
| | - Marina Vannucci
- Department of Statistics, Rice University, Houston, TX, USA.
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Robb M, Hobbs JK, Woodiga SA, Shapiro-Ward S, Suits MDL, McGregor N, Brumer H, Yesilkaya H, King SJ, Boraston AB. Molecular Characterization of N-glycan Degradation and Transport in Streptococcus pneumoniae and Its Contribution to Virulence. PLoS Pathog 2017; 13:e1006090. [PMID: 28056108 PMCID: PMC5215778 DOI: 10.1371/journal.ppat.1006090] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/27/2016] [Indexed: 11/19/2022] Open
Abstract
The carbohydrate-rich coating of human tissues and cells provide a first point of contact for colonizing and invading bacteria. Commensurate with N-glycosylation being an abundant form of protein glycosylation that has critical functional roles in the host, some host-adapted bacteria possess the machinery to process N-linked glycans. The human pathogen Streptococcus pneumoniae depolymerizes complex N-glycans with enzymes that sequentially trim a complex N-glycan down to the Man3GlcNAc2 core prior to the release of the glycan from the protein by endo-β-N-acetylglucosaminidase (EndoD), which cleaves between the two GlcNAc residues. Here we examine the capacity of S. pneumoniae to process high-mannose N-glycans and transport the products. Through biochemical and structural analyses we demonstrate that S. pneumoniae also possesses an α-(1,2)-mannosidase (SpGH92). This enzyme has the ability to trim the terminal α-(1,2)-linked mannose residues of high-mannose N-glycans to generate Man5GlcNAc2. Through this activity SpGH92 is able to produce a substrate for EndoD, which is not active on high-mannose glycans with α-(1,2)-linked mannose residues. Binding studies and X-ray crystallography show that NgtS, the solute binding protein of an ABC transporter (ABCNG), is able to bind Man5GlcNAc, a product of EndoD activity, with high affinity. Finally, we evaluated the contribution of EndoD and ABCNG to growth of S. pneumoniae on a model N-glycosylated glycoprotein, and the contribution of these enzymes and SpGH92 to virulence in a mouse model. We found that both EndoD and ABCNG contribute to growth of S. pneumoniae, but that only SpGH92 and EndoD contribute to virulence. Therefore, N-glycan processing, but not transport of the released glycan, is required for full virulence in S. pneumoniae. To conclude, we synthesize our findings into a model of N-glycan processing by S. pneumoniae in which both complex and high-mannose N-glycans are targeted, and in which the two arms of this degradation pathway converge at ABCNG. Streptococcus pneumoniae (pneumococcus) is a bacterium that causes extensive morbidity and mortality in humans. Vaccines and antibiotics are effective forms of prevention and treatment, respectively, but present challenges as it is a constant race to vaccinate against the enormous and ever evolving pool of different serotypes of the bacterium while resistance to antibiotics continues to trend upwards. It is thus necessary to better understand the molecular aspects of the host-pneumococcus interaction in order to inform the potential generation of alternative treatment strategies. S. pneumoniae relies on its ability to process the carbohydrates presented on the surface of host cells for full-virulence. In this study, we examine the capability of the bacterium to process high-mannose N-linked sugars, a heretofore unknown ability for S. pneumoniae. The results show that the pneumococcal genome encodes enzymes capable of processing these sugars and that, remarkably, the initiating reaction performed by an enzyme that removes terminal α-(1,2)-linked mannose residues is critical to virulence in a mouse model. This study illuminates an extensive pathway in S. pneumoniae that targets N-linked sugars and is key to the host-pathogen interaction, therefore revealing a potential target for therapeutic intervention.
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Affiliation(s)
- Melissa Robb
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Joanne K. Hobbs
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Shireen A. Woodiga
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Sarah Shapiro-Ward
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Michael D. L. Suits
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Nicholas McGregor
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories and Department of Chemistry, University of British Columbia, 2185 East Mall, Vancouver, British Columbia, Canada
| | - Hasan Yesilkaya
- Department of Infection, Immunity & Inflammation, University of Leicester, Leicester, United Kingdom
| | - Samantha J. King
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children’s Hospital, Columbus, Ohio, United States of America
| | - Alisdair B. Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- * E-mail:
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Abstract
Complex carbohydrates are ubiquitous in all kingdoms of life. As major components of the plant cell wall they constitute both a rich renewable carbon source for biotechnological transformation into fuels, chemicals and materials, and also form an important energy source as part of a healthy human diet. In both contexts, there has been significant, sustained interest in understanding how microbes transform these substrates. Classical perspectives of microbial polysaccharide degradation are currently being augmented by recent advances in the discovery of lytic polysaccharide monooxygenases (LPMOs) and polysaccharide utilization loci (PULs). Fundamental discoveries in carbohydrate enzymology are both advancing biological understanding, as well as informing applications in industrial biomass conversion and modulation of the human gut microbiota to mediate health benefits.
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50
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de Freitas MCR, Resende JA, Ferreira-Machado AB, Saji GDRQ, de Vasconcelos ATR, da Silva VL, Nicolás MF, Diniz CG. Exploratory Investigation of Bacteroides fragilis Transcriptional Response during In vitro Exposure to Subinhibitory Concentration of Metronidazole. Front Microbiol 2016; 7:1465. [PMID: 27703449 PMCID: PMC5028390 DOI: 10.3389/fmicb.2016.01465] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 09/01/2016] [Indexed: 12/29/2022] Open
Abstract
Bacteroides fragilis, member from commensal gut microbiota, is an important pathogen associated to endogenous infections and metronidazole remains a valuable antibiotic for the treatment of these infections, although bacterial resistance is widely reported. Considering the need of a better understanding on the global mechanisms by which B. fragilis survive upon metronidazole exposure, we performed a RNA-seq transcriptomic approach with validation of gene expression results by qPCR. Bacteria strains were selected after in vitro subcultures with subinhibitory concentration (SIC) of the drug. From a wild type B. fragilis ATCC 43859 four derivative strains were selected: first and fourth subcultures under metronidazole exposure and first and fourth subcultures after drug removal. According to global gene expression analysis, 2,146 protein coding genes were identified, of which a total of 1,618 (77%) were assigned to a Gene Ontology term (GO), indicating that most known cellular functions were taken. Among these 2,146 protein coding genes, 377 were shared among all strains, suggesting that they are critical for B. fragilis survival. In order to identify distinct expression patterns, we also performed a K-means clustering analysis set to 15 groups. This analysis allowed us to detect the major activated or repressed genes encoding for enzymes which act in several metabolic pathways involved in metronidazole response such as drug activation, defense mechanisms against superoxide ions, high expression level of multidrug efflux pumps, and DNA repair. The strains collected after metronidazole removal were functionally more similar to those cultured under drug pressure, reinforcing that drug-exposure lead to drastic persistent changes in the B. fragilis gene expression patterns. These results may help to elucidate B. fragilis response during metronidazole exposure, mainly at SIC, contributing with information about bacterial survival strategies under stress conditions in their environment.
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Affiliation(s)
- Michele C R de Freitas
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Juliana A Resende
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Alessandra B Ferreira-Machado
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Guadalupe D R Q Saji
- Laboratório de Bioinformática and Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Ana T R de Vasconcelos
- Laboratório de Bioinformática and Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Vânia L da Silva
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
| | - Marisa F Nicolás
- Laboratório de Bioinformática and Laboratório Nacional de Computação Científica Petrópolis, Brazil
| | - Cláudio G Diniz
- Departamento de Parasitologia, Microbiologia e Imunologia, Universidade Federal de Juiz de Fora Juiz de Fora, Brazil
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