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Cui X, Fu Z, Wang H, Yu W, Han F. Cloning and characterization of a hyaluronate lyase EsHyl8 from Escherichia sp. A99. Protein Expr Purif 2024; 223:106551. [PMID: 38997076 DOI: 10.1016/j.pep.2024.106551] [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: 04/07/2024] [Revised: 06/30/2024] [Accepted: 07/09/2024] [Indexed: 07/14/2024]
Abstract
Hyaluronidase, an enzyme that degrades hyaluronic acid (HA), is utilized in clinical settings to facilitate drug diffusion, manage extravasation, and address injection-related complications linked to HA-based fillers. In this study, a novel hyaluronate lyase EsHyl8 was cloned, expressed, and characterized from Escherichia sp. A99 of human intestinal origin. This lyase belongs to polysaccharide lyase (PL) family 8, and showed specific activity towards HA. EsHyl8 exhibited optimal degradation at 40 °C and pH 6.0. EsHyl8 exhibited a high activity of 376.32 U/mg among hyaluronidases of human gut microorganisms. EsHyl8 was stable at 37 °C and remained about 70 % of activity after incubation at 37 °C for 24 h, demonstrating excellent thermostability. The activity of EsHyl8 was inhibited by Zn2+, Cu2+, Fe3+, and SDS. EsHyl8 was an endo-type enzyme whose end-product was unsaturated disaccharide. This study enhances our understanding of hyaluronidases from human gut microorganisms.
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Affiliation(s)
- Xiuli Cui
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Zheng Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Hainan Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Feng Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Qingdao Marine Science and Technology Center, Qingdao, 266237, China; Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao 266003, China; Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China.
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Fu Y, Fu Z, Yu J, Wang H, Zhang Y, Liu M, Wang X, Yu W, Han F. Biochemical Characterization of Hyaluronate Lyase CpHly8 from an Intestinal Microorganism Clostridium perfringens G1121. Appl Biochem Biotechnol 2024:10.1007/s12010-024-05025-y. [PMID: 39235659 DOI: 10.1007/s12010-024-05025-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2024] [Indexed: 09/06/2024]
Abstract
Hyaluronic acid (HA) is an important component of extracellular matrices (ECM) and a linear polysaccharide involved in various physiological and pathological processes within the biological system. Several pathogens exploit HA degradation within the extracellular matrix to facilitate infection. While many intestinal microorganisms play significant roles in HA utilization in the human body, there remains a scarcity of related studies. This paper addressed this gap by screening intestinal microorganisms capable of degrading HA, resulting in the isolation of Clostridium perfringens G1121, which had been demonstrated the ability to degrade HA. Subsequent genome sequencing and analysis of C. perfringens G1121 revealed its utilization of the polysaccharide utilization loci of HA (PULHA), which was obtained by horizontal gene transfer. The PULHA contains a sequence encoding a hyaluronic acid-specific degradation enzyme designated CpHly8, belonging to polysaccharide lyase family 8. The specific activity of CpHly8 towards HA was 142.98 U/mg, with the optimum reaction temperature and pH observed at 50℃ and 6.0, respectively. The final product of HA degradation by CpHly8 was unsaturated hyaluronic acid disaccharide. Moreover, subcutaneous diffusion experiments with trypan blue in mice revealed that CpHly8 effectively promoted subcutaneous diffusion and sustained its effects long-term, suggesting its potential application as an adjunct in drug delivery. Overall, our study enriches our understanding of intestinal microbial degradation of HA, provides new evidence for horizontal gene transfer among intestinal microorganisms, and confirms that CpHly8 is a promising candidate for intestinal microbial hyaluronidase.
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Affiliation(s)
- Yongqing Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Zheng Fu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Jing Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Hainan Wang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Yuzhu Zhang
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Mei Liu
- School of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266071, China
| | - Xiaolei Wang
- School of Marine Life Sciences, Ocean University of China, Qingdao, 266003, China
- Laboratory for Marine Ecology and Environmental Science, Laoshan Laboratory, Qingdao, 266071, China
| | - Wengong Yu
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China
| | - Feng Han
- School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Qingdao Marine Science and Technology Center, Qingdao, 266237, China.
- Key Laboratory of Marine Drugs, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
- Shandong Provincial Key Laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, 266003, China.
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Rønne ME, Dybdahl Andersen C, Teze D, Petersen AB, Fredslund F, Stender EGP, Chaberski EK, Holck J, Aachmann FL, Welner DH, Svensson B. Action and cooperation in alginate degradation by three enzymes from the human gut bacterium Bacteroides eggerthii DSM 20697. J Biol Chem 2024; 300:107596. [PMID: 39032652 PMCID: PMC11381880 DOI: 10.1016/j.jbc.2024.107596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/12/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Alginate is a polysaccharide consumed by humans in edible seaweed and different foods where it is applied as a texturizing hydrocolloid or in encapsulations of drugs and probiotics. While gut bacteria are found to utilize and ferment alginate to health-beneficial short-chain fatty acids, knowledge on the details of the molecular reactions is sparse. Alginates are composed of mannuronic acid (M) and its C-5 epimer guluronic acid (G). An alginate-related polysaccharide utilization locus (PUL) has been identified in the gut bacterium Bacteroides eggerthii DSM 20697. The PUL encodes two polysaccharide lyases (PLs) from the PL6 (BePL6) and PL17 (BePL17) families as well as a KdgF-like metalloprotein (BeKdgF) known to catalyze ring-opening of 4,5-unsaturated monouronates yielding 4-deoxy-l-erythro-5-hexoseulose uronate (DEH). B. eggerthii DSM 20697 does not grow on alginate, but readily proliferates with a lag phase of a few hours in the presence of an endo-acting alginate lyase A1-I from the marine bacterium Sphingomonas sp. A1. The B. eggerthii lyases are both exo-acting and while BePL6 is strictly G-block specific, BePL17 prefers M-blocks. BeKdgF retained 10-27% activity in the presence of 0.1-1 mM EDTA. X-ray crystallography was used to investigate the three-dimensional structure of BeKdgF, based on which a catalytic mechanism was proposed to involve Asp102, acting as acid/base having pKa of 5.9 as determined by NMR pH titration. BePL6 and BePL17 cooperate in alginate degradation with BeKdgF linearizing producing 4,5-unsaturated monouronates. Their efficiency of alginate degradation was much enhanced by the addition of the A1-I alginate lyase.
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Affiliation(s)
- Mette E Rønne
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Christian Dybdahl Andersen
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - David Teze
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark; Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Agnes Beenfeldt Petersen
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Folmer Fredslund
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Emil G P Stender
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Evan Kirk Chaberski
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Jesper Holck
- Enzyme Technology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Ditte Hededam Welner
- Enzyme Engineering and Structural Biology, Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
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Ma XQ, Wang B, Wei W, Tan FC, Su H, Zhang JZ, Zhao CY, Zheng HJ, Feng YQ, Shen W, Yang JB, Li FL. Alginate oligosaccharide assimilation by gut microorganisms and the potential role in gut inflammation alleviation. Appl Environ Microbiol 2024; 90:e0004624. [PMID: 38563787 PMCID: PMC11107165 DOI: 10.1128/aem.00046-24] [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: 01/08/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024] Open
Abstract
Dietary fiber metabolism by gut microorganisms plays important roles in host physiology and health. Alginate, the major dietary fiber of daily diet seaweeds, is drawing more attention because of multiple biological activities. To advance the understanding of alginate assimilation mechanism in the gut, we show the presence of unsaturated alginate oligosaccharides (uAOS)-specific alginate utilization loci (AUL) in human gut microbiome. As a representative example, a working model of the AUL from the gut microorganism Bacteroides clarus was reconstructed from biochemistry and transcriptome data. The fermentation of resulting monosaccharides through Entner-Doudoroff pathway tunes the metabolism of short-chain fatty acids and amino acids. Furthermore, we show that uAOS feeding protects the mice against dextran sulfate sodium-induced acute colitis probably by remodeling gut microbiota and metabolome. IMPORTANCE Alginate has been included in traditional Chinese medicine and daily diet for centuries. Recently discovered biological activities suggested that alginate-derived alginate oligosaccharides (AOS) might be an active ingredient in traditional Chinese medicine, but how these AOS are metabolized in the gut and how it affects health need more information. The study on the working mechanism of alginate utilization loci (AUL) by the gut microorganism uncovers the role of unsaturated alginate oligosaccharides (uAOS) assimilation in tuning short-chain fatty acids and amino acids metabolism and demonstrates that uAOS metabolism by gut microorganisms results in a variation of cell metabolites, which potentially contributes to the physiology and health of gut.
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Affiliation(s)
- Xiao-Qing Ma
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Bing Wang
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wei
- Innovation Center of Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fang-Cheng Tan
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Hang Su
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Jun-Zhe Zhang
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Chen-Yang Zhao
- Innovation Center of Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hua-Jun Zheng
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
| | - Yan-Qin Feng
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Wei Shen
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jin-Bo Yang
- Innovation Center of Marine Drug Screening & Evaluation, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Fu-Li Li
- Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
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Tannock GW. Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation. Microbiol Mol Biol Rev 2024; 88:e0012722. [PMID: 38126754 PMCID: PMC10966955 DOI: 10.1128/mmbr.00127-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Dapa T, Xavier KB. Effect of diet on the evolution of gut commensal bacteria. Gut Microbes 2024; 16:2369337. [PMID: 38904092 PMCID: PMC11195494 DOI: 10.1080/19490976.2024.2369337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
The gut microbiota, comprising trillions of diverse microorganisms inhabiting the intestines of animals, forms a complex and indispensable ecosystem with profound implications for the host's well-being. Its functions include contributing to developing the host's immune response, aiding in nutrient digestion, synthesizing essential compounds, acting as a barrier against pathogen invasion, and influencing the development or regression of various pathologies. The dietary habits of the host directly impact this intricate community of gut microbes. Diet influences the composition and function of the gut microbiota through alterations in gene expression, enzymatic activity, and metabolome. While the impact of diet on gut ecology is well-established, the investigation into the relationship between dietary consumption and microbial genotypic diversity has been limited. This review provides an overview of the relationship between diet and gut microbiota, emphasizing the impact of host nutrition on both short- and long-term evolution in the mammalian gut. It is evident that the evolution of the gut microbiota occurs even on short timescales through the acquisition of novel mutations, within the gut bacteria of individual hosts. Consequently, we discuss the importance of considering alterations in bacterial genomic diversity when analyzing microbiota-dependent effects on host physiology. Future investigations into the various microbiota-related traits shall greatly benefit from a deeper understanding of commensal bacterial evolutionary adaptation.
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Affiliation(s)
- Tanja Dapa
- Andalusian Center for Developmental Biology (CABD), Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University/CSIC/Junta de Andalucía, Seville, Spain
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
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Rønne ME, Tandrup T, Madsen M, Hunt CJ, Myers PN, Moll JM, Holck J, Brix S, Strube ML, Aachmann FL, Wilkens C, Svensson B. Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate. Appl Environ Microbiol 2023; 89:e0118523. [PMID: 37791757 PMCID: PMC10617595 DOI: 10.1128/aem.01185-23] [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: 07/20/2023] [Accepted: 08/03/2023] [Indexed: 10/05/2023] Open
Abstract
Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.
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Affiliation(s)
- Mette E. Rønne
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Tobias Tandrup
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikkel Madsen
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Cameron J. Hunt
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pernille N. Myers
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Janne M. Moll
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Disease Systems Immunology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mikael L. Strube
- Department of Biotechnology and Biomedicine, Bacterial Ecophysiology and Biotechnology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Finn L. Aachmann
- Department of Biotechnology and Food Science, Norwegian Biopolymer Laboratory (NOBIPOL), NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Casper Wilkens
- Department of Biotechnology and Biomedicine, Enzyme Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Biotechnology and Biomedicine, Structural Enzymology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Enzyme and Protein Chemistry, Technical University of Denmark, Kgs. Lyngby, Denmark
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Shannon E, Conlon M, Hayes M. The Prebiotic Effect of Australian Seaweeds on Commensal Bacteria and Short Chain Fatty Acid Production in a Simulated Gut Model. Nutrients 2022; 14:nu14102163. [PMID: 35631304 PMCID: PMC9146517 DOI: 10.3390/nu14102163] [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] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/20/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Diet is known to affect the composition and metabolite production of the human gut microbial community, which in turn is linked with the health and immune status of the host. Whole seaweeds (WH) and their extracts contain prebiotic components such as polysaccharides (PS) and polyphenols (PP). In this study, the Australian seaweeds, Phyllospora comosa, Ecklonia radiata, Ulva ohnoi, and their PS and PP extracts were assessed for potential prebiotic activities using an in vitro gut model that included fresh human faecal inoculum. 16S rRNA sequencing post gut simulation treatment revealed that the abundance of several taxa of commensal bacteria within the phylum Firmicutes linked with short chain fatty acid (SCFA) production, and gut and immune function, including the lactic acid producing order Lactobacillales and the chief butyrate-producing genera Faecalibacteria, Roseburia, Blautia, and Butyricicoccus were significantly enhanced by the inclusion of WH, PS and PP extracts. After 24 h fermentation, the abundance of total Firmicutes ranged from 57.35−81.55% in the WH, PS and PP samples, which was significantly greater (p ≤ 0.01) than the inulin (INU) polysaccharide control (32.50%) and the epigallocatechingallate (EGCG) polyphenol control (67.13%); with the exception of P. comosa PP (57.35%), which was significantly greater than INU only. However, all WH, PS and PP samples also increased the abundance of the phylum Proteobacteria; while the abundance of the phylum Actinobacteria was decreased by WH and PS samples. After 24 h incubation, the total and individual SCFAs present, including butyric, acetic and propionic acids produced by bacteria fermented with E. radiata and U. ohnoi, were significantly greater than the SCFAs identified in the INU and EGCG controls. Most notably, total SCFAs in the E. radiata PS and U. ohnoi WH samples were 227.53 and 208.68 µmol/mL, respectively, compared to only 71.05 µmol/mL in INU and 7.76 µmol/mL in the EGCG samples. This study demonstrates that whole seaweeds and their extracts have potential as functional food ingredients to support normal gut and immune function.
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Affiliation(s)
- Emer Shannon
- Teagasc Food Biosciences, Ashtown Food Research Centre, Dunsinea Lane, Ashtown, D15 KN3K Dublin, Ireland;
- The Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Adelaide, SA 5000, Australia;
- Correspondence: ; Tel.: +353-1-8059980
| | - Michael Conlon
- The Commonwealth Scientific and Industrial Research Organisation, Health and Biosecurity, Adelaide, SA 5000, Australia;
| | - Maria Hayes
- Teagasc Food Biosciences, Ashtown Food Research Centre, Dunsinea Lane, Ashtown, D15 KN3K Dublin, Ireland;
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La Rosa SL, Ostrowski MP, Vera-Ponce de León A, McKee LS, Larsbrink J, Eijsink VG, Lowe EC, Martens EC, Pope PB. Glycan processing in gut microbiomes. Curr Opin Microbiol 2022; 67:102143. [PMID: 35338908 DOI: 10.1016/j.mib.2022.102143] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 12/16/2022]
Abstract
Microbiomes and their enzymes process many of the nutrients accessible in the gastrointestinal tract of bilaterians and play an essential role in host health and nutrition. In this review, we describe recent insights into nutrient processing in microbiomes across three exemplary yet contrasting gastrointestinal ecosystems (humans, ruminants and insects), with focus on bacterial mechanisms for the utilization of common and atypical dietary glycans as well as host-derived mucus glycans. In parallel, we discuss findings from multi-omic studies that have provided new perspectives on understanding glycan-dependent interactions and the complex food-webs of microbial populations in their natural habitat. Using key examples, we emphasize how increasing understanding of glycan processing by gut microbiomes can provide critical insights to assist 'microbiome reprogramming', a growing field that seeks to leverage diet to improve animal growth and host health.
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Affiliation(s)
| | - Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Arturo Vera-Ponce de León
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1433, Norway
| | - Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, 106 91, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
| | - Vincent G Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1433, Norway
| | | | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, 48109, MI, USA
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1433, Norway; Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1433, Norway
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10
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Metabolism of a hybrid algal galactan by members of the human gut microbiome. Nat Chem Biol 2022; 18:501-510. [PMID: 35289327 DOI: 10.1038/s41589-022-00983-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022]
Abstract
Native porphyran is a hybrid of porphryan and agarose. As a common element of edible seaweed, this algal galactan is a frequent component of the human diet. Bacterial members of the human gut microbiota have acquired polysaccharide utilization loci (PULs) that enable the metabolism of porphyran or agarose. However, the molecular mechanisms that underlie the deconstruction and use of native porphyran remains incompletely defined. Here, we have studied two human gut bacteria, porphyranolytic Bacteroides plebeius and agarolytic Bacteroides uniformis, that target native porphyran. This reveals an exo-based cycle of porphyran depolymerization that incorporates a keystone sulfatase. In both PULs this cycle also works together with a PUL-encoded agarose depolymerizing machinery to synergistically reduce native porphyran to monosaccharides. This provides a framework for understanding the deconstruction of a hybrid algal galactan, and insight into the competitive and/or syntrophic relationship of gut microbiota members that target rare nutrients.
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11
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Pudlo NA, Pereira GV, Parnami J, Cid M, Markert S, Tingley JP, Unfried F, Ali A, Varghese NJ, Kim KS, Campbell A, Urs K, Xiao Y, Adams R, Martin D, Bolam DN, Becher D, Eloe-Fadrosh EA, Schmidt TM, Abbott DW, Schweder T, Hehemann JH, Martens EC. Diverse events have transferred genes for edible seaweed digestion from marine to human gut bacteria. Cell Host Microbe 2022; 30:314-328.e11. [PMID: 35240043 PMCID: PMC9096808 DOI: 10.1016/j.chom.2022.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 11/03/2021] [Accepted: 02/02/2022] [Indexed: 12/16/2022]
Abstract
Humans harbor numerous species of colonic bacteria that digest fiber polysaccharides in commonly consumed terrestrial plants. More recently in history, regional populations have consumed edible macroalgae seaweeds containing unique polysaccharides. It remains unclear how extensively gut bacteria have adapted to digest these nutrients. Here, we show that the ability of gut bacteria to digest seaweed polysaccharides is more pervasive than previously appreciated. Enrichment-cultured Bacteroides harbor previously discovered genes for seaweed degradation, which have mobilized into several members of this genus. Additionally, other examples of marine bacteria-derived genes, and their mobile DNA elements, are involved in gut microbial degradation of seaweed polysaccharides, including genes in gut-resident Firmicutes. Collectively, these results uncover multiple separate events that have mobilized the genes encoding seaweed-degrading-enzymes into gut bacteria. This work further underscores the metabolic plasticity of the human gut microbiome and global exchange of genes in the context of dietary selective pressures.
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Affiliation(s)
- Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Jaagni Parnami
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Melissa Cid
- Max Planck Institute for Marine Biology, Bremen, Germany
| | - Stephanie Markert
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jeffrey P Tingley
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Frank Unfried
- Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Ahmed Ali
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Kwi S Kim
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Austin Campbell
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Karthik Urs
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yao Xiao
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan Adams
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Duña Martin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - D Wade Abbott
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB, Canada
| | - Thomas Schweder
- Pharmaceutical Biotechnology, University of Greifswald, 17487 Greifswald, Germany; Institute of Marine Biotechnology, 17489 Greifswald, Germany
| | - Jan Hendrik Hehemann
- Max Planck Institute for Marine Biology, Bremen, Germany; University of Bremen, Center for Marine Environmental Sciences (MARUM), 28359 Bremen, Germany.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA.
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12
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Pardesi B, Roberton AM, Lee KC, Angert ER, Rosendale DI, Boycheva S, White WL, Clements KD. Distinct microbiota composition and fermentation products indicate functional compartmentalization in the hindgut of a marine herbivorous fish. Mol Ecol 2022; 31:2494-2509. [PMID: 35152505 PMCID: PMC9306998 DOI: 10.1111/mec.16394] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/04/2022] [Accepted: 02/07/2022] [Indexed: 11/28/2022]
Abstract
Many marine herbivorous fishes harbour diverse microbial communities in the hindgut that can play important roles in host health and nutrition. Kyphosus sydneyanus is a temperate marine herbivorous fish that feeds predominantly on brown seaweeds. We employed 16S rRNA gene amplicon sequencing and gas chromatography to characterize microbial communities and their metabolites in different hindgut regions of six K. sydneyanus. Measurements were confined to three distal sections of the intestine, labelled III, IV and V from anterior to posterior. A total of 625 operational taxonomic units from 20 phyla and 123 genera were obtained. Bacteroidota, Firmicutes and Proteobacteria were the major phyla in mean relative abundance, which varied along the gut. Firmicutes (76%) was the most dominant group in section III, whereas Bacteroidota (69.3%) dominated section V. Total short‐chain fatty acid (SCFA) concentration was highest in sections IV and V, confirming active fermentation in these two most distal sections. The abundance of Bacteroidota correlated with propionate concentration in section V, while Firmicutes positively correlated with formate in sections III and IV. Acetate levels were highest in sections IV and V, which correlated with abundance of Bacteroidota. Despite differences in gut microbial community composition, SCFA profiles were consistent between individual fish in the different hindgut regions of K. sydneyanus, although proportions of SCFAs differed among gut sections. These findings demonstrate functional compartmentalization of the hindgut microbial community, highlighting the need for regional sampling when interpreting overall microbiome function. These results support previous work suggesting that hindgut microbiota in marine herbivorous fish are important to nutrition in some host species by converting dietary carbohydrates into metabolically useful SCFAs.
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Affiliation(s)
- Bikiran Pardesi
- School of Biological Sciences University of Auckland Auckland New Zealand
| | | | - Kevin C. Lee
- Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
| | - Esther R. Angert
- Department of Microbiology Cornell University Ithaca NY 14853 USA
| | - Douglas I. Rosendale
- Plant & Food Research Ltd Palmerston North New Zealand
- Anagenix Ltd Parnell, Auckland 1052 New Zealand
| | - Svetlana Boycheva
- School of Biological Sciences University of Auckland Auckland New Zealand
- Biotelliga, Parnell, Auckland 1052 New Zealand
| | - William Lindsey White
- School of Science Faculty of Health and Environmental Sciences Auckland University of Technology Auckland New Zealand
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13
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de Oliveira BFR, Lopes IR, Canellas ALB, Muricy G, Jackson SA, Dobson ADW, Laport MS. Genomic and in silico protein structural analyses provide insights into marine polysaccharide-degrading enzymes in the sponge-derived Pseudoalteromonas sp. PA2MD11. Int J Biol Macromol 2021; 191:973-995. [PMID: 34555402 DOI: 10.1016/j.ijbiomac.2021.09.076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/01/2021] [Accepted: 09/11/2021] [Indexed: 10/20/2022]
Abstract
Active heterotrophic metabolism is a critical metabolic role performed by sponge-associated microorganisms, but little is known about their capacity to metabolize marine polysaccharides (MPs). Here, we investigated the genome of the sponge-derived Pseudoalteromonas sp. strain PA2MD11 focusing on its macroalgal carbohydrate-degrading potential. Carbohydrate-active enzymes (CAZymes) for the depolymerization of agar and alginate were found in PA2MD11's genome, including glycoside hydrolases (GHs) and polysaccharide lyases (PLs) belonging to families GH16, GH50 and GH117, and PL6 and PL17, respectively. A gene potentially encoding a sulfatase was also identified, which may play a role in the strain's ability to consume carrageenans. The complete metabolism of agar and alginate by PA2MD11 could also be predicted and was consistent with the results obtained in physiological assays. The polysaccharide utilization locus (PUL) potentially involved in the metabolism of agarose contained mobile genetic elements from other marine Gammaproteobacteria and its unusual larger size might be due to gene duplication events. Homology modelling and structural protein analyses of the agarases, alginate lyases and sulfatase depicted clear conservation of catalytic machinery and protein folding together with suitable industrially-relevant features. Pseudoalteromonas sp. PA2MD11 is therefore a source of potential MP-degrading biocatalysts for biorefinery applications and in the preparation of pharmacologically-active oligosaccharides.
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Affiliation(s)
- Bruno Francesco Rodrigues de Oliveira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil; School of Microbiology, University College Cork, T12 Y960 Cork, Ireland
| | - Isabelle Rodrigues Lopes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil
| | - Anna Luiza Bauer Canellas
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil
| | - Guilherme Muricy
- Departamento de Invertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro, Quinta da Boa Vista, s/n°, São Cristóvão, 20940-040 Rio de Janeiro, RJ, Brazil
| | - Stephen Anthony Jackson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland; Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Alan D W Dobson
- School of Microbiology, University College Cork, T12 Y960 Cork, Ireland; Environmental Research Institute, University College Cork, T23 XE10 Cork, Ireland
| | - Marinella Silva Laport
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Cidade Universitária, 21941-590 Rio de Janeiro, Brazil.
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14
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Essential contributions of food hydrocolloids and phospholipid liposomes to the formation of carriers for controlled delivery of biologically active substances via the gastrointestinal tract. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106890] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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15
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Xu F, Cha QQ, Zhang YZ, Chen XL. Degradation and Utilization of Alginate by Marine Pseudoalteromonas: a Review. Appl Environ Microbiol 2021; 87:e0036821. [PMID: 34160244 PMCID: PMC8357284 DOI: 10.1128/aem.00368-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Alginate, which is mainly produced by brown algae and decomposed by heterotrophic bacteria, is an important marine organic carbon source. The genus Pseudoalteromonas contains diverse forms of heterotrophic bacteria that are widely distributed in marine environments and are an important group in alginate degradation. In this review, the diversity of alginate-degrading Pseudoalteromonas is introduced, and the characteristics of Pseudoalteromonas alginate lyases, including their sequences, enzymatic properties, structures, and catalytic mechanisms, and the synergistic effect of Pseudoalteromonas alginate lyases on alginate degradation are introduced. The acquisition of the alginate degradation capacity and the alginate utilization pathways of Pseudoalteromonas are also introduced. This paper provides a comprehensive overview of alginate degradation by Pseudoalteromonas, which will contribute to the understanding of the degradation and recycling of marine algal polysaccharides driven by marine bacteria.
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Affiliation(s)
- Fei Xu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Qian-Qian Cha
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
- Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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16
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Seaweed Supplementation Failed to Affect Fecal Microbiota and Metabolome as Well as Fecal IgA and Apparent Nutrient Digestibility in Adult Dogs. Animals (Basel) 2021; 11:ani11082234. [PMID: 34438692 PMCID: PMC8388444 DOI: 10.3390/ani11082234] [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: 06/23/2021] [Revised: 07/20/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022] Open
Abstract
The present study investigated in dogs the dietary effects of intact seaweeds on some fecal bacterial populations and metabolites, fecal IgA and apparent total tract digestibility (ATTD). Ten healthy adult dogs were enrolled in a 5 × 5 replicated Latin square design to evaluate five dietary treatments: control diet (CD); CD + Ascophyllum nodosum; CD + Undaria pinnatifida; CD + Saccharina japonica; CD + Palmaria palmata (n replicates per treatment = 10). Seaweeds were added to food at a daily dose of 15 g/kg. The CD contained silica as a digestion marker. Each feeding period lasted 28 d, with a 7 d wash-out in between. Feces were collected at days 21 and 28 of each period for chemical and microbiological analyses. Fecal samples were collected during the last five days of each period for ATTD assessment. Dogs showed good health conditions throughout the study. The fecal chemical parameters, fecal IgA and nutrient ATTD were not influenced by algal supplementation. Similarly, microbiological analyses did not reveal any effect by seaweed ingestion. In conclusion, algal supplementation at a dose of 15 g/kg of diet failed to exert noticeable effects on the canine fecal parameters evaluated in the present study.
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17
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Jouanneau D, Klau LJ, Larocque R, Jaffrennou A, Duval G, Le Duff N, Roret T, Jeudy A, Aachmann FL, Czjzek M, Thomas F. Structure-function analysis of a new PL17 oligoalginate lyase from the marine bacterium Zobellia galactanivorans DsijT. Glycobiology 2021; 31:1364-1377. [PMID: 34184062 PMCID: PMC8600288 DOI: 10.1093/glycob/cwab058] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/19/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022] Open
Abstract
Alginate is a major compound of brown macroalgae and as such an important carbon and energy source for heterotrophic marine bacteria. Despite the rather simple composition of alginate only comprising mannuronate and guluronate units, these bacteria feature complex alginolytic systems that can contain up to seven alginate lyases. This reflects the necessity of large enzyme systems for the complete degradation of the abundant substrate. Numerous alginate lyases have been characterized. They belong to different polysaccharide lyase (PL) families, but only one crystal structure of a family 17 (PL17) alginate lyase has been reported to date, namely Alg17c from the gammaproteobacterium Saccharophagus degradans. Biochemical and structural characterizations are helpful to link sequence profiles to function, evolution of functions and niche-specific characteristics. Here, we combined detailed biochemical and crystallographic analysis of AlyA3, a PL17 alginate lyase from the marine flavobacteria Zobellia galactanivorans DsijT, providing the first structure of a PL17 in the Bacteroidetes phylum. AlyA3 is exo-lytic and highly specific of mannuronate stretches. As part of an “alginate utilizing locus”, its activity is complementary to that of other characterized alginate lyases from the same bacterium. Structural comparison with Alg17c highlights a common mode of action for exo-lytic cleavage of the substrate, strengthening our understanding of the PL17 catalytic mechanism. We show that unlike Alg17c, AlyA3 contains an inserted flexible loop at the entrance to the catalytic groove, likely involved in substrate recognition, processivity and turn over.
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Affiliation(s)
- Diane Jouanneau
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Leesa J Klau
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Robert Larocque
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Agathe Jaffrennou
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Ghislain Duval
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Nolwen Le Duff
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Thomas Roret
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, Roscoff, France
| | - Alexandra Jeudy
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Finn L Aachmann
- Norwegian Biopolymer Laboratory (NOBIPOL), Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Sem Sælands vei 6/8, N-7491 Trondheim, Norway
| | - Mirjam Czjzek
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - François Thomas
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
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18
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Shannon E, Conlon M, Hayes M. Seaweed Components as Potential Modulators of the Gut Microbiota. Mar Drugs 2021; 19:358. [PMID: 34201794 PMCID: PMC8303941 DOI: 10.3390/md19070358] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/20/2021] [Accepted: 06/20/2021] [Indexed: 12/11/2022] Open
Abstract
Macroalgae, or seaweeds, are a rich source of components which may exert beneficial effects on the mammalian gut microbiota through the enhancement of bacterial diversity and abundance. An imbalance of gut bacteria has been linked to the development of disorders such as inflammatory bowel disease, immunodeficiency, hypertension, type-2-diabetes, obesity, and cancer. This review outlines current knowledge from in vitro and in vivo studies concerning the potential therapeutic application of seaweed-derived polysaccharides, polyphenols and peptides to modulate the gut microbiota through diet. Polysaccharides such as fucoidan, laminarin, alginate, ulvan and porphyran are unique to seaweeds. Several studies have shown their potential to act as prebiotics and to positively modulate the gut microbiota. Prebiotics enhance bacterial populations and often their production of short chain fatty acids, which are the energy source for gastrointestinal epithelial cells, provide protection against pathogens, influence immunomodulation, and induce apoptosis of colon cancer cells. The oral bioaccessibility and bioavailability of seaweed components is also discussed, including the advantages and limitations of static and dynamic in vitro gastrointestinal models versus ex vivo and in vivo methods. Seaweed bioactives show potential for use in prevention and, in some instances, treatment of human disease. However, it is also necessary to confirm these potential, therapeutic effects in large-scale clinical trials. Where possible, we have cited information concerning these trials.
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Affiliation(s)
- Emer Shannon
- Food Biosciences, Teagasc Food Research Centre, Ashtown, D15 KN3K Dublin, Ireland;
- CSIRO Health and Biosecurity, Kintore Avenue, Adelaide, SA 5000, Australia;
| | - Michael Conlon
- CSIRO Health and Biosecurity, Kintore Avenue, Adelaide, SA 5000, Australia;
| | - Maria Hayes
- Food Biosciences, Teagasc Food Research Centre, Ashtown, D15 KN3K Dublin, Ireland;
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19
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Fu T, Pan L, Shang Q, Yu G. Fermentation of alginate and its derivatives by different enterotypes of human gut microbiota: Towards personalized nutrition using enterotype-specific dietary fibers. Int J Biol Macromol 2021; 183:1649-1659. [PMID: 34048831 DOI: 10.1016/j.ijbiomac.2021.05.135] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/08/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022]
Abstract
Alginate and its derivatives are widely used as food additives and dietary fibers. Previous studies indicated that alginate, polyguluronate (PG) and polymannuronate acid (PM) could be fermented by human gut microbiota. However, how different compositions of the microbiota may affect the fermentation outcomes of these polysaccharides remains unknown. Here we show that Bacteroides-dominated microbiota (Bacteroides enterotype) is more proficient at degrading and utilizing PG and PM as compared to Prevotella-dominated (Prevotella enterotype) and Escherichia-dominated microbiota (Escherichia enterotype). Enterotype dictates the fermentation outcomes of the three fibers and the amount of short-chain fatty acids (SCFAs) that are produced. Fermentation of alginate and PM by Bacteroides-dominated microbiota produced the highest amount of total SCFAs and butyrate. Our study demonstrates an enterotype-specific effect of microbiota on the fermentation of alginate and its derivatives and highlights that personalized nutrition using dietary fibers should be tailored according to individual's composition of the gut microbiome.
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Affiliation(s)
- Tianyu Fu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Lin Pan
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Qingsen Shang
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Qingdao Marine Biomedical Research Institute, Qingdao 266071, China.
| | - Guangli Yu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China.
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20
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Hou Y, Li B, Feng G, Zhang C, He J, Li H, Zhu J. Responses of bacterial communities and organic matter degradation in surface sediment to Macrobrachium nipponense bioturbation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 759:143534. [PMID: 33293082 DOI: 10.1016/j.scitotenv.2020.143534] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/24/2020] [Accepted: 10/25/2020] [Indexed: 06/12/2023]
Abstract
The excessive accumulation of organic matter (OM) in sediments in aquaculture ponds is a potential environmental threat due to the risk of endogenous water pollution and eutrophication. From the perspective of inhibiting OM accumulation to prevent endogenous water pollution, the present study investigated the OM degradation states, variations of bacterial communities and basic environmental factors in sediments with/without Macrobrachium nipponense treatment/control groups in triplicate for effects of bioturbation on OM degradation in 90-day incubation. The total organic carbon (TOC) and total nitrogen (TN) in the M. nipponense treatment were higher than in the control at the 30th and 60th days, while no significant differences between treatment and control were found at the end of the experiment. Significantly higher oxidation-reduction potential (ORP) and more extensively degraded OM were observed in the M. nipponense treatment. Eleven significantly differential bacterial taxa were enriched in the sediments of M. nipponense treatment, of which eight (Actinobacteria, Chitinophagales, Chitinophagaceae, Flavihumibacter, Marinilabiliaceae, Cytophaga xylanolytica group, Christensenellaceae, and Christensenellaceae R-7 group) were significantly correlated with at least two OM degradation indicators. The functional groups chemoheterotrophy, aerobic chemoheterotrophy, xylanolysis, ureolysis, and intracellular parasites were enhanced by M. nipponense and were negatively correlated with OM degradation indictors. Overall, the M. nipponense bioturbation effectively increased the ORP to provide better conditions for OM degradation, altered the taxonomic composition and functional groups to enhance the bacterial ability for OM degradation, and finally promoted the OM degradation of the surface sediment in an artificial aquaculture system.
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Affiliation(s)
- Yiran Hou
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Bing Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Gongcheng Feng
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi 214081, China
| | - Chengfeng Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Haidong Li
- Zhejiang Ocean University, School of Fishery, Zhoushan 316022, China
| | - Jian Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
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21
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Effect of in vitro digestion-fermentation of Ca(II)-alginate beads containing sugar and biopolymers over global antioxidant response and short chain fatty acids production. Food Chem 2020; 333:127483. [DOI: 10.1016/j.foodchem.2020.127483] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 12/15/2022]
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22
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Singh RP, Bhaiyya R, Khandare K, Tingirikari JMR. Macroalgal dietary glycans: potential source for human gut bacteria and enhancing immune system for better health. Crit Rev Food Sci Nutr 2020; 62:1674-1695. [PMID: 33190530 DOI: 10.1080/10408398.2020.1845605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Macroalgae are the diverse group of photosynthetic algae found at the intertidal regions of oceans. Recent advances suggest that macroalgal derived glycans have tremendous potential to maintain gut microbiome and immune system. The human gut bacteria harbor unique arsenals for utilizing a variety of macroalgal glycans, and produce a variety of oligosaccharides in vivo. Those oligosaccharides interact with immune cell receptors, and also are available for microbial fermentation, thus play magnificent roles in balancing the gut homeostasis. However, this area of research is still in infancy condition in term to understand their molecular interactions. For wooing this area, we urge to emphasize more studies on mechanistic level sympathetic of depolymerizing marine dietary glycans by gut bacteria and elucidating molecular aspect of glycans to cell receptors interactions. This will invent new nutraceutical strategies to purposefully manipulate the microbial composition to improve health. Therefore, review focuses on the recent development of mechanistic understanding of human gut bacterial communities for utilizing macroalgal derived glycans. Recent trends of application of glycans in modulating immune system at mechanistic level and their available evidences are discussed.
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Affiliation(s)
- Ravindra Pal Singh
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Punjab, India
| | - Raja Bhaiyya
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Punjab, India
| | - Kiran Khandare
- Food and Nutritional Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Punjab, India
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23
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Glowacki RWP, Martens EC. If you eat it, or secrete it, they will grow: the expanding list of nutrients utilized by human gut bacteria. J Bacteriol 2020; 203:JB.00481-20. [PMID: 33168637 PMCID: PMC8092160 DOI: 10.1128/jb.00481-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to persist, successful bacterial inhabitants of the human gut need to adapt to changing nutrient conditions, which are influenced by host diet and a variety of other factors. For members of the Bacteroidetes and several other phyla, this has resulted in diversification of a variety of enzyme-based systems that equip them to sense and utilize carbohydrate-based nutrients from host, diet, and bacterial origin. In this review, we focus first on human gut Bacteroides and describe recent findings regarding polysaccharide utilization loci (PULs) and the mechanisms of the multi-protein systems they encode, including their regulation and the expanding diversity of substrates that they target. Next, we highlight previously understudied substrates such as monosaccharides, nucleosides, and Maillard reaction products that can also affect the gut microbiota by feeding symbionts that possess specific systems for their metabolism. Since some pathogens preferentially utilize these nutrients, they may represent nutrient niches competed for by commensals and pathogens. Finally, we address recent work to describe nutrient acquisition mechanisms in other important gut species such as those belonging to the Gram-positive anaerobic phyla Actinobacteria and Firmicutes, as well as the Proteobacteria Because gut bacteria contribute to many aspects of health and disease, we showcase advances in the field of synthetic biology, which seeks to engineer novel, diet-controlled nutrient utilization pathways within gut symbionts to create rationally designed live therapeutics.
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Affiliation(s)
- Robert W. P. Glowacki
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Eric C. Martens
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, USA
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24
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Mouritsen OG, Rhatigan P, Cornish ML, Critchley AT, Pérez-Lloréns JL. Saved by seaweeds: phyconomic contributions in times of crises. JOURNAL OF APPLIED PHYCOLOGY 2020; 33:443-458. [PMID: 33191980 PMCID: PMC7647873 DOI: 10.1007/s10811-020-02256-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 05/07/2023]
Abstract
Seaweeds (macroalgae) are, together with microalgae, main contributors to the Earth's production of organic matter and atmospheric oxygen as well as fixation of carbon dioxide. In addition, they contain a bounty of fibres and minerals, as well as macro- and micronutrients that can serve both technical and medicinal purposes, as well as be a healthy and nutritious food for humans and animals. It is therefore natural that seaweeds and humans have had a myriad of interwoven relationships both on evolutionary timescales as well as in recent millennia and centuries all the way into the Anthropocene. It is no wonder that seaweeds have also entered and served as a saviour for humankind around the globe in many periods of severe needs and crises. Indeed, they have sometimes been the last resort, be it during times of famine, warfare, outbreak of diseases, nuclear accidents, or as components of securing the fabric of social stability. The present topical review presents testimony from the history of human interaction with seaweeds to the way humankind has, over and over again, been 'saved by seaweeds'. It remains a historical fact that in extreme conditions, such as shortage and wars, humans have turned to seaweeds in times of 'needs must' and created new opportunities for their uses in order to mitigate disasters. Lessons to be learned from this history can be used as reminders and inspiration, and as a guide as how to turn to seaweeds in current and inevitable, future times of crises, not least for the present needs of how to deal with changing climates and the pressing challenges of sustainable and healthy eating.
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Affiliation(s)
- Ole G. Mouritsen
- Department of Food Science, Taste for Life, Design and Consumer Behaviour, University of Copenhagen, 26 Rolighedsvej, DK-1958 Frederiksberg, Denmark
| | - Prannie Rhatigan
- Irish Seaweed Kitchen, Streedagh House, Streedagh, Grange, Co., Sligo, Ireland
| | - M. Lynn Cornish
- James S. Craigie Research Centre, Acadian Seaplants Limited, Cornwallis, NS B0S1A0 Canada
| | - Alan T. Critchley
- Verschuren Centre for Sustainability in Energy and Environment, Cape Breton University, Sydney, Nova Scotia Canada
| | - José Lucas Pérez-Lloréns
- Instituto Universitario de Investigación Marina (INMAR), Universidad de Cádiz, Av. República Saharaui s/n. 11510, Puerto Real, Cádiz, Spain
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25
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Ferrer-González FX, Widner B, Holderman NR, Glushka J, Edison AS, Kujawinski EB, Moran MA. Resource partitioning of phytoplankton metabolites that support bacterial heterotrophy. ISME JOURNAL 2020; 15:762-773. [PMID: 33097854 PMCID: PMC8027193 DOI: 10.1038/s41396-020-00811-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 10/02/2020] [Accepted: 10/09/2020] [Indexed: 11/09/2022]
Abstract
The communities of bacteria that assemble around marine microphytoplankton are predictably dominated by Rhodobacterales, Flavobacteriales, and families within the Gammaproteobacteria. Yet whether this consistent ecological pattern reflects the result of resource-based niche partitioning or resource competition requires better knowledge of the metabolites linking microbial autotrophs and heterotrophs in the surface ocean. We characterized molecules targeted for uptake by three heterotrophic bacteria individually co-cultured with a marine diatom using two strategies that vetted the exometabolite pool for biological relevance by means of bacterial activity assays: expression of diagnostic genes and net drawdown of exometabolites, the latter detected with mass spectrometry and nuclear magnetic resonance using novel sample preparation approaches. Of the more than 36 organic molecules with evidence of bacterial uptake, 53% contained nitrogen (including nucleosides and amino acids), 11% were organic sulfur compounds (including dihydroxypropanesulfonate and dimethysulfoniopropionate), and 28% were components of polysaccharides (including chrysolaminarin, chitin, and alginate). Overlap in phytoplankton-derived metabolite use by bacteria in the absence of competition was low, and only guanosine, proline, and N-acetyl-D-glucosamine were predicted to be used by all three. Exometabolite uptake pattern points to a key role for ecological resource partitioning in the assembly marine bacterial communities transforming recent photosynthate.
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Affiliation(s)
| | - Brittany Widner
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Nicole R Holderman
- Department of Biochemistry and Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - John Glushka
- Department of Biochemistry and Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Arthur S Edison
- Department of Biochemistry and Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, 02543, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, 30602, USA.
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26
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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: 11] [Impact Index Per Article: 2.8] [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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27
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Gotteland M, Riveros K, Gasaly N, Carcamo C, Magne F, Liabeuf G, Beattie A, Rosenfeld S. The Pros and Cons of Using Algal Polysaccharides as Prebiotics. Front Nutr 2020; 7:163. [PMID: 33072794 PMCID: PMC7536576 DOI: 10.3389/fnut.2020.00163] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 12/12/2022] Open
Abstract
Macroalgae stand out for their high content of dietary fiber (30–75%) that include soluble, sulfated (fucoidan, agaran, carrageenan, and ulvan) and non-sulfated (laminaran and alginate) polysaccharides. Many studies indicate that these compounds exert varied biological activities and health-promoting effects and for this reason, there is a growing interest for using them in food products. The aim of this review was to critically evaluate prebiotic properties of algal polysaccharides, i.e., their ability to exert biological activities by modulating the composition and/or diversity of gut microbiota (GM). Pre-clinical studies show that the non-sulfated alginate and laminaran are well-fermented by GM, promoting the formation of short chain fatty acids (SCFAs) including butyrate, and preventing that of harmful putrefactive compounds (NH3, phenol, p-cresol, indole and H2S). Alginate increases Bacteroides, Bifidobacterium, and Lactobacillus species while laminaran mostly stimulates Bacteroides sp. Results with sulfated polysaccharides are more questionable. Agarans are poorly fermentable but agarose-oligosaccharides exhibit an interesting prebiotic potential, increasing butyrate-producing bacteria and SCFAs. Though carrageenan-oligosaccharides are also fermented, their use is currently limited due to safety concerns. Regarding fucoidan, only one study reports SCFAs production, suggesting that it is poorly fermented. Its effect on GM does not indicate a clear pattern, making difficult to conclude whether it is beneficial or not. Notably, fucoidan impact on H2S production has not been evaluated, though some studies report it increases sulfate-reducing bacteria. Ulvan is badly fermented by GM and some studies show that part of its sulfate is dissimilated to H2S, which could affect colonic mitochondrial function. Accordingly, these results support the use of laminaran, alginate and agaro-oligosaccharides as prebiotics while more studies are necessary regarding that of fucoidan, carrageenan and ulvan. However, the realization of clinical trials is necessary to confirm such prebiotic properties in humans.
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Affiliation(s)
- Martin Gotteland
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile.,Department of Human Nutrition, Institute of Nutrition and Food Technology (INTA), University of Chile, Santiago, Chile.,Millennium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Karla Riveros
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Naschla Gasaly
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Constanza Carcamo
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Fabien Magne
- Microbiology and Mycology Program, Institute of Biomedical Sciences (ICBM), Faculty of Medicine, University of Chile, Santiago, Chile
| | - Gianella Liabeuf
- Department of Nutrition, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Alejandra Beattie
- Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile.,Centro de Investigación para la Conservación de Ecosistemas Australes, Punta Arenas, Chile
| | - Sebastián Rosenfeld
- Laboratorio de Ecosistemas Marinos Antárticos y Subantárticos, Universidad de Magallanes, Punta Arenas, Chile.,Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Instituto de Ecología y Biodiversidad, Santiago, Chile
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28
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Zhou HX, Xu SS, Yin XJ, Wang FL, Li Y. Characterization of a New Bifunctional and Cold-Adapted Polysaccharide Lyase (PL) Family 7 Alginate Lyase from Flavobacterium sp. Mar Drugs 2020; 18:E388. [PMID: 32722647 PMCID: PMC7460543 DOI: 10.3390/md18080388] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 07/23/2020] [Accepted: 07/24/2020] [Indexed: 12/14/2022] Open
Abstract
Alginate oligosaccharides produced by enzymatic degradation show versatile physiological functions and biological activities. In this study, a new alginate lyase encoding gene alyS02 from Flavobacterium sp. S02 was recombinantly expressed at a high level in Yarrowia lipolytica, with the highest extracellular activity in the supernatant reaching 36.8 ± 2.1 U/mL. AlyS02 was classified in the polysaccharide lyase (PL) family 7. The optimal reaction temperature and pH of this enzyme were 30 °C and 7.6, respectively, indicating that AlyS02 is a cold-adapted enzyme. Interestingly, AlyS02 contained more than 90% enzyme activity at 25 °C, higher than other cold-adapted enzymes. Moreover, AlyS02 is a bifunctional alginate lyase that degrades both polyG and polyM, producing di- and trisaccharides from alginate. These findings suggest that AlyS02 would be a potent tool for the industrial applications.
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Affiliation(s)
- Hai-Xiang Zhou
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China;
| | - Shan-Shan Xu
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China;
| | - Xue-Jing Yin
- Qingdao Mental Health Center, Qingdao University, Qingdao 266034, China;
| | - Feng-Long Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China;
| | - Yang Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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29
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You L, Gong Y, Li L, Hu X, Brennan C, Kulikouskaya V. Beneficial effects of three brown seaweed polysaccharides on gut microbiota and their structural characteristics: An overview. Int J Food Sci Technol 2019. [DOI: 10.1111/ijfs.14408] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Lijun You
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640China
| | - Yufeng Gong
- School of Food Science and Engineering South China University of Technology 381 Wushan Road Guangzhou Guangdong 510640China
| | - Laihao Li
- Key Laboratory of Aquatic Product Processing Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou 510300China
| | - Xiao Hu
- Key Laboratory of Aquatic Product Processing Ministry of Agriculture and Rural Affairs South China Sea Fisheries Research Institute Chinese Academy of Fishery Sciences Guangzhou 510300China
| | - Charles Brennan
- Department of Wine, Food and Molecular Biosciences Lincoln University Lincoln, Canterbury 7608New Zealand
| | - Viktoryia Kulikouskaya
- Institute of Chemistry of New Materials National Academy of Sciences of Belarus 36F. Skaryna str. Minsk 220141Belarus
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30
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García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T, Kyrpides NC, Hahnke RL, Göker M. Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 2019; 10:2083. [PMID: 31608019 PMCID: PMC6767994 DOI: 10.3389/fmicb.2019.02083] [Citation(s) in RCA: 190] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 08/23/2019] [Indexed: 11/25/2022] Open
Abstract
Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.
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Affiliation(s)
- Marina García-López
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Jan P. Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brian J. Tindall
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Sabine Gronow
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tanja Woyke
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Nikos C. Kyrpides
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, United States
| | - Richard L. Hahnke
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Markus Göker
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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31
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Boto L, Pineda M, Pineda R. Potential impacts of horizontal gene transfer on human health and physiology and how anthropogenic activity can affect it. FEBS J 2019; 286:3959-3967. [PMID: 31495055 DOI: 10.1111/febs.15054] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/01/2019] [Accepted: 09/03/2019] [Indexed: 12/19/2022]
Abstract
Horizontal gene transfer (HGT) is widespread among prokaryotes driving their evolution. In this paper, we review the potential impact in humans of the HGT between prokaryotes living in close association with humans in two scenarios: horizontal transfer in human microbiomes and transfer between microbes living in human managed environments. Although our vision is focused on the possible impact of these transfers in the propagation of antibiotic resistance genes or pathogenicity determinants, we also discuss possible human physiological adaptations via gene transfer between resident and occasional bacteria in the human microbiome.
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Affiliation(s)
- Luis Boto
- Departamento DE Biodiversidad y Biologia Evolutiva, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
| | - Manuel Pineda
- Grupo Fisiologia Molecular y Biotecnologia de Plantas, Universidad dE Cordoba, Spain
| | - Rafael Pineda
- Instituto Maimonides de Investigacion Biomedica de Cordoba, Spain.,Departamento de Biologia Celular, Fisiologia e Inmunologia, Universidad de Cordoba, Spain
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Stender EGP, Dybdahl Andersen C, Fredslund F, Holck J, Solberg A, Teze D, Peters GHJ, Christensen BE, Aachmann FL, Welner DH, Svensson B. Structural and functional aspects of mannuronic acid-specific PL6 alginate lyase from the human gut microbe Bacteroides cellulosilyticus. J Biol Chem 2019; 294:17915-17930. [PMID: 31530640 PMCID: PMC6879350 DOI: 10.1074/jbc.ra119.010206] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/16/2019] [Indexed: 01/28/2023] Open
Abstract
Alginate is a linear polysaccharide from brown algae consisting of 1,4-linked β-d-mannuronic acid (M) and α-l-guluronic acid (G) arranged in M, G, and mixed MG blocks. Alginate was assumed to be indigestible in humans, but bacteria isolated from fecal samples can utilize alginate. Moreover, genomes of some human gut microbiome-associated bacteria encode putative alginate-degrading enzymes. Here, we genome-mined a polysaccharide lyase family 6 alginate lyase from the gut bacterium Bacteroides cellulosilyticus (BcelPL6). The structure of recombinant BcelPL6 was solved by X-ray crystallography to 1.3 Å resolution, revealing a single-domain, monomeric parallel β-helix containing a 10-step asparagine ladder characteristic of alginate-converting parallel β-helix enzymes. Substitutions of the conserved catalytic site residues Lys-249, Arg-270, and His-271 resulted in activity loss. However, imidazole restored the activity of BcelPL6-H271N to 2.5% that of the native enzyme. Molecular docking oriented tetra-mannuronic acid for syn attack correlated with M specificity. Using biochemical analyses, we found that BcelPL6 initially releases unsaturated oligosaccharides of a degree of polymerization of 2-7 from alginate and polyM, which were further degraded to di- and trisaccharides. Unlike other PL6 members, BcelPL6 had low activity on polyMG and none on polyG. Surprisingly, polyG increased BcelPL6 activity on alginate 7-fold. LC-electrospray ionization-MS quantification of products and lack of activity on NaBH4-reduced octa-mannuronic acid indicated that BcelPL6 is an endolyase that further degrades the oligosaccharide products with an intact reducing end. We anticipate that our results advance predictions of the specificity and mode of action of PL6 enzymes.
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Affiliation(s)
- Emil G P Stender
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Christian Dybdahl Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Folmer Fredslund
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Jesper Holck
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Amalie Solberg
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Günther H J Peters
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Bjørn E Christensen
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Finn L Aachmann
- Department of Biotechnology and Food Science, NTNU, Norwegian University of Science and Technology, N-7491 Trondheim, Norway
| | - Ditte H Welner
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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Cherry P, Yadav S, Strain CR, Allsopp PJ, McSorley EM, Ross RP, Stanton C. Prebiotics from Seaweeds: An Ocean of Opportunity? Mar Drugs 2019; 17:E327. [PMID: 31159359 PMCID: PMC6627129 DOI: 10.3390/md17060327] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/27/2019] [Accepted: 05/29/2019] [Indexed: 02/07/2023] Open
Abstract
Seaweeds are an underexploited and potentially sustainable crop which offer a rich source of bioactive compounds, including novel complex polysaccharides, polyphenols, fatty acids, and carotenoids. The purported efficacies of these phytochemicals have led to potential functional food and nutraceutical applications which aim to protect against cardiometabolic and inflammatory risk factors associated with non-communicable diseases, such as obesity, type 2 diabetes, metabolic syndrome, cardiovascular disease, inflammatory bowel disease, and some cancers. Concurrent understanding that perturbations of gut microbial composition and metabolic function manifest throughout health and disease has led to dietary strategies, such as prebiotics, which exploit the diet-host-microbe paradigm to modulate the gut microbiota, such that host health is maintained or improved. The prebiotic definition was recently updated to "a substrate that is selectively utilised by host microorganisms conferring a health benefit", which, given that previous discussion regarding seaweed prebiotics has focused upon saccharolytic fermentation, an opportunity is presented to explore how non-complex polysaccharide components from seaweeds may be metabolised by host microbial populations to benefit host health. Thus, this review provides an innovative approach to consider how the gut microbiota may utilise seaweed phytochemicals, such as polyphenols, polyunsaturated fatty acids, and carotenoids, and provides an updated discussion regarding the catabolism of seaweed-derived complex polysaccharides with potential prebiotic activity. Additional in vitro screening studies and in vivo animal studies are needed to identify potential prebiotics from seaweeds, alongside untargeted metabolomics to decipher microbial-derived metabolites from seaweeds. Furthermore, controlled human intervention studies with health-related end points to elucidate prebiotic efficacy are required.
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Affiliation(s)
- Paul Cherry
- Nutrition Innovation Centre for Food and Health, Ulster University, Cromore Road, Coleraine, Co. Londonderry BT52 1SA, UK.
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
| | - Supriya Yadav
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
| | - Conall R Strain
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
| | - Philip J Allsopp
- Nutrition Innovation Centre for Food and Health, Ulster University, Cromore Road, Coleraine, Co. Londonderry BT52 1SA, UK.
| | - Emeir M McSorley
- Nutrition Innovation Centre for Food and Health, Ulster University, Cromore Road, Coleraine, Co. Londonderry BT52 1SA, UK.
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
- College of Science, Engineering and Food Science, University College Cork, Cork T12 K8AF, Ireland.
| | - Catherine Stanton
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, P61 C996, Ireland.
- APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland.
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