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Detain J, Besaury L. Degradation of lignocellulose by different bacterial and fungal co-cultures. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 7:100271. [PMID: 39291138 PMCID: PMC11406349 DOI: 10.1016/j.crmicr.2024.100271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2024] Open
Abstract
Long seen as non-valorisable waste, agricultural co-products are increasingly used in biorefinery processes. Co-culture appears as new trend for to improve the degradation of lignocellulose and improve the production of bioproducts. The goal of the study was to setup inter-domain co-cultures with high capabilities of lignocellulose degradation using a pluridisciplinary approach combining bioinformatics, enzymology, transcriptomics. Different individual lignocellulolytic strains: Trichoderma reesei QM6a and three bacteria (Streptomyces coelicolor A3(2), Rhizobium sp.XylPr11 and Sphingobacterium prati AraPr2 affiliated from different phyla) were used in that study . Synergic activities have been observed and quantified in co-culture conditions, particularly for xylanases and peroxidases activities. The enzymatic activities for the co-cultures in the most interesting co-culture (T. reesei QM6a/S. coelicolor A3(2)) reached more up to 2 IU/mL and 430 IU/mL respectively for the xylanase and peroxidase. Furthermore, ATR-FTIR analysis showed a real impact of co-culture condition on the substrate compared to the monoculture specially for hemicellulose degradation. Transcriptomics of S. coelicolor A3(2) either in mono or co-culture showed a relative similar pattern profile whatever the condition analysed with a specific overexpression of certain CAZyme genes involved in glycolysis due to the hydrolytic role played by the fungal partner. This work provided the proof of concept for technological feasibility, pertinence and usefulness of interdomain co-culture.
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Affiliation(s)
- Julian Detain
- Université de Reims Champagne Ardennes, INRAE, FARE, UMR A 614, Chaire AFERE, 51097 Reims, France
| | - Ludovic Besaury
- Université de Reims Champagne Ardennes, INRAE, FARE, UMR A 614, Chaire AFERE, 51097 Reims, France
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Golisch B, Cordeiro RL, Fraser ASC, Briggs J, Stewart WA, Van Petegem F, Brumer H. The molecular basis of cereal mixed-linkage β-glucan utilization by the human gut bacterium Segatella copri. J Biol Chem 2024; 300:107625. [PMID: 39122003 PMCID: PMC11418011 DOI: 10.1016/j.jbc.2024.107625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Mixed-linkage β(1,3)/β(1,4)-glucan (MLG) is abundant in the human diet through the ingestion of cereal grains and is widely associated with healthful effects on metabolism and cholesterol levels. MLG is also a major source of fermentable glucose for the human gut microbiota (HGM). Bacteria from the family Prevotellaceae are highly represented in the HGM of individuals who eat plant-rich diets, including certain indigenous people and vegetarians in postindustrial societies. Here, we have defined and functionally characterized an exemplar Prevotellaceae MLG polysaccharide utilization locus (MLG-PUL) in the type-strain Segatella copri (syn. Prevotella copri) DSM 18205 through transcriptomic, biochemical, and structural biological approaches. In particular, structure-function analysis of the cell-surface glycan-binding proteins and glycoside hydrolases of the S. copri MLG-PUL revealed the molecular basis for glycan capture and saccharification. Notably, syntenic MLG-PULs from human gut, human oral, and ruminant gut Prevotellaceae are distinguished from their counterparts in Bacteroidaceae by the presence of a β(1,3)-specific endo-glucanase from glycoside hydrolase family 5, subfamily 4 (GH5_4) that initiates MLG backbone cleavage. The definition of a family of homologous MLG-PULs in individual species enabled a survey of nearly 2000 human fecal microbiomes using these genes as molecular markers, which revealed global population-specific distributions of Bacteroidaceae- and Prevotellaceae-mediated MLG utilization. Altogether, the data presented here provide new insight into the molecular basis of β-glucan metabolism in the HGM, as a basis for informing the development of approaches to improve the nutrition and health of humans and other animals.
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Affiliation(s)
- Benedikt Golisch
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rosa Lorizolla Cordeiro
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander S C Fraser
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jonathon Briggs
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - William A Stewart
- 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
| | - Filip Van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada; Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
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Hameleers L, Pijning T, Gray BB, Fauré R, Jurak E. Novel β-galactosidase activity and first crystal structure of Glycoside Hydrolase family 154. N Biotechnol 2024; 80:1-11. [PMID: 38163476 DOI: 10.1016/j.nbt.2023.12.011] [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: 07/31/2023] [Revised: 12/27/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Polysaccharide Utilization Loci (PULs) are physically linked gene clusters conserved in the Gram-negative phylum of Bacteroidota and are valuable sources for Carbohydrate Active enZyme (CAZyme) discovery. This study focuses on BD-β-Gal, an enzyme encoded in a metagenomic PUL and member of the Glycoside Hydrolase family 154 (GH154). BD-β-Gal showed exo-β-galactosidase activity with regiopreference for hydrolyzing β-d-(1,6) glycosidic linkages. Notably, it exhibited a preference for d-glucopyranosyl (d-Glcp) over d-galactopyranosyl (d-Galp) and d-fructofuranosyl (d-Fruf) at the reducing end of the investigated disaccharides. In addition, we determined the high resolution crystal structure of BD-β-Gal, thus providing the first structural characterization of a GH154 enzyme. Surprisingly, this revealed an (α/α)6 topology, which has not been observed before for β-galactosidases. BD-β-Gal displayed low structural homology with characterized CAZymes, but conservation analysis suggested that the active site was located in a central cavity, with conserved E73, R252, and D253 as putative catalytic residues. Interestingly, BD-β-Gal has a tetrameric structure and a flexible loop from a neighboring protomer may contribute to its reaction specificity. Finally, we showed that the founding member of GH154, BT3677 from Bacteroides thetaiotaomicron, described as β-glucuronidase, displayed exo-β-galactosidase activity like BD-β-Gal but lacked a tetrameric structure.
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Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Tjaard Pijning
- Department of Biomolecular X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, Groningen 9747 AG, the Netherlands
| | - Brandon B Gray
- Department of Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands
| | - Régis Fauré
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Edita Jurak
- Department of Bioproduct Engineering, Engineering and Technology institute Groningen (ENTEG), University of Groningen, Nijenborgh 4, Groningen 9747 AG, the Netherlands.
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Felber J, Gross B, Rahrisch A, Waltersbacher E, Trips E, Schröttner P, Fitze G, Schultz J. Bacterial pathogens in pediatric appendicitis: a comprehensive retrospective study. Front Cell Infect Microbiol 2023; 13:1027769. [PMID: 37228669 PMCID: PMC10205019 DOI: 10.3389/fcimb.2023.1027769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/30/2023] [Indexed: 05/27/2023] Open
Abstract
Background Appendicitis is a frequent condition, with peak incidences in the second decade of life. Its pathogenesis is under debate, but bacterial infections are crucial, and antibiotic treatment remains essential. Rare bacteria are accused of causing complications, and various calculated antibiotics are propagated, yet there is no comprehensive microbiological analysis of pediatric appendicitis. Here we review different pre-analytic pathways, identify rare and common bacterial pathogens and their antibiotic resistances, correlate clinical courses, and evaluate standard calculated antibiotics in a large pediatric cohort. Method We reviewed 579 patient records and microbiological results of intraoperative swabs in standard Amies agar media or fluid samples after appendectomies for appendicitis between May 2011 and April 2019. Bacteria were cultured and identified via VITEK 2 or MALDI-TOF MS. Minimal inhibitory concentrations were reevaluated according to EUCAST 2022. Results were correlated to clinical courses. Results Of 579 analyzed patients, in 372 patients we got 1330 bacterial growths with resistograms. 1259 times, bacteria could be identified to species level. 102 different bacteria could be cultivated. 49% of catarrhal and 52% of phlegmonous appendices resulted in bacterial growth. In gangrenous appendicitis, only 38% remained sterile, while this number reduced to 4% after perforation. Many fluid samples remained sterile even when unsterile swabs had been taken simultaneously. 40 common enteral genera were responsible for 76.5% of bacterial identifications in 96.8% of patients. However, 69 rare bacteria were found in 187 patients without specifically elevated risk for complications. Conclusion Amies agar gel swabs performed superior to fluid samples and should be a standard in appendectomies. Even catarrhal appendices were only sterile in 51%, which is interesting in view of a possible viral cause. According to our resistograms, the best in vitro antibiotic was imipenem with 88.4% susceptible strains, followed by piperacillin-tazobactam, cefuroxime with metronidazole, and ampicillin-sulbactam to which only 21.6% of bacteria were susceptible. Bacterial growths and higher resistances correlate to an elevated risk of complications. Rare bacteria are found in many patients, but there is no specific consequence regarding antibiotic susceptibility, clinical course, or complications. Prospective, comprehensive studies are needed to further elicit pediatric appendicitis microbiology and antibiotic treatment.
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Affiliation(s)
- Julia Felber
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Benedikt Gross
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Arend Rahrisch
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Eric Waltersbacher
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Evelyn Trips
- Coordination Centre for Clinical Trials, Faculty of Medicine Carl Gustav Carus, Technical University of Dresden, Dresden, Germany
| | - Percy Schröttner
- Institute for Microbiology and Virology, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Guido Fitze
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
| | - Jurek Schultz
- Department of Pediatric Surgery, University Hospital Dresden – Technical University of Dresden, Dresden, Germany
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Liu Y, Lei S, Hou R, Li D, Wan X, Cai H, Chen G. Tea polysaccharides from Taiping Houkui may serve as a potential candidate for regulation of lipid metabolism: Roles of gut microbiota and metabolite in vitro. J Funct Foods 2023. [DOI: 10.1016/j.jff.2023.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
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Chen L, Sun M, Xu D, Gao Z, Shi Y, Wang S, Zhou Y. Gut microbiome of captive wolves is more similar to domestic dogs than wild wolves indicated by metagenomics study. Front Microbiol 2022; 13:1027188. [PMID: 36386659 PMCID: PMC9663663 DOI: 10.3389/fmicb.2022.1027188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 11/24/2022] Open
Abstract
Adaptation during the domestication from wolves (Canis lupus) to dogs (Canis lupus familiaris) is a debated ecological topic. Changes in food and environment are major divergences in the domestication of dogs. Gut microbes play an important role in animal adaptation to the food and environmental changes. In this study, shotgun sequencing was performed to compare the species diversity and functional diversity of gut microbes in wild wolves (group CLW, n = 3), captive wolves (group CLC, n = 4), and domestic dogs (group CLF, n = 4). The results found that Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and Bacteroides, Fusobacterium, Prevotella, Megamonas, Paraprevotella, Faecalibacterium, Clostridium were the most abundant genera in the gut of wolves and dogs. Groups CLW, CLC and CLF have shown significant difference in gut microbial species diversity and functional diversity. Bacteroides, Fusobacterium and Faecalibacterium were most abundant genera in groups CLW, CLC and CLF, respectively. Their abundance varied significantly among groups. Compared to the wild wolves, the intestinal microbiol genes of domestic dogs were significantly enriched in the carbohydrate metabolism pathway of KEGG database. One hundred and seventy-seven enzymes were detected with significantly higher abundance in group CLF than that in group CLW, and 49 enzymes showed extremely significant higher abundance in group CLF than that in group CLW (q < 0.01) base on the function abundance annotated in CAZy database. It is noteworthy that there were also significant differences in the abundance of 140 enzymes between groups CLC and CLW (q < 0.05). Clustering analysis based on both the species and the function abundance of intestinal microbiota all found that groups CLC and CLF clustered into one branch, while samples from group CLW clustered into the other branch. This result suggests that captive wolves are more similar to domestic dogs than wild wolves in both species composition and function composition of intestinal microbiota.
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