1
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Tang J, Zuo W, Guo L, Han Z, Yang C, Han B, Dai L, Zhang X, Zhou X. Synergistic pectin deconstruction is a prerequisite for mutualistic interactions between honeybee gut bacteria. Nat Commun 2024; 15:6937. [PMID: 39138170 PMCID: PMC11322527 DOI: 10.1038/s41467-024-51365-y] [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: 11/30/2023] [Accepted: 08/02/2024] [Indexed: 08/15/2024] Open
Abstract
The honeybee gut microbiome is crucial for degrading diverse pollen glycans. Yet it is unclear how this process shapes the interactions among bacteria. Here, we demonstrate a conditional mutualistic interaction between strains of two honeybee gut bacteria Bifidobacterium asteroides and Gilliamella apicola. When co-occurring in vitro and in vivo, Bifidobacterium provides complementary demethylation service to promote Gilliamella growth on methylated homogalacturonan, an enriched polysaccharide of pectin. In exchange, Gilliamella shares digestive products with Bifidobacterium, through which a positive interaction is established. This positive interaction vanishes when Bifidobacterium is not required on a non-methylated diet. Results from biochemical and gene expression analyses combined with model simulation further suggest that the ratio change of the two major homogalacturonan breakdown products, galacturonic acid (GalA) and di-GalA, determines the bacterial interaction. This study unravels how glycan metabolism may shape the interactions between honeybee gut bacteria.
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Affiliation(s)
- Junbo Tang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Lizhen Guo
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Zhihao Han
- Department of Biomedical Engineering, School of Engineering, China Pharmaceutical University, Nanjing, China
| | - Chengfeng Yang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Sanya Institute of China Agricultural University, Hainan, China
| | - Benfeng Han
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China
- Department of Microbiology and Immunology, College of Biological Science, China Agricultural University, Beijing, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Xue Zhang
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China.
| | - Xin Zhou
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, China.
- Sanya Institute of China Agricultural University, Hainan, China.
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2
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Gao R, Wu T, Stock AM. A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides. mBio 2024; 15:e0122024. [PMID: 38842315 PMCID: PMC11253607 DOI: 10.1128/mbio.01220-24] [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: 04/23/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Hybrid two-component systems (HTCSs) comprise a major class of transcription regulators of polysaccharide utilization genes in Bacteroides. Distinct from classical two-component systems in which signal transduction is carried out by intermolecular phosphotransfer between a histidine kinase (HK) and a cognate response regulator (RR), HTCSs contain the membrane sensor HK and the RR transcriptional regulator within a single polypeptide chain. Tethering the DNA-binding domain (DBD) of the RR with the dimeric HK domain in an HTCS could potentially promote dimerization of the DBDs and would thus require a mechanism to suppress DNA-binding activity in the absence of stimulus. Analysis of phosphorylation and DNA-binding activities of several HTCSs from Bacteroides thetaiotaomicron revealed a DBD suppression mechanism in which an inhibitory interaction between the DBD and the phosphoryl group-accepting receiver domain (REC) decreases autophosphorylation rates of HTCS-RECs and represses DNA-binding activities in the absence of phosphorylation. Sequence analyses and structure predictions identified a highly conserved sequence motif correlated with a conserved inhibitory domain arrangement of REC and DBD. The presence of the motif, as in most HTCSs, or its absence, in a small subset of HTCSs, is likely predictive of two distinct regulatory mechanisms evolved for different glycans. Substitutions within the conserved motif relieve the inhibitory interaction and result in elevated DNA-binding activities in the absence of phosphorylation. Our data suggest a fundamental regulatory mechanism shared by most HTCSs to suppress DBD activities using a conserved inhibitory interdomain arrangement to overcome the challenge of the fused HK and RR components. IMPORTANCE Different dietary and host-derived complex carbohydrates shape the gut microbial community and impact human health. In Bacteroides, the prevalent gut bacteria genus, utilization of these diverse carbohydrates relies on different gene clusters that are under sophisticated control by various signaling systems, including the hybrid two-component systems (HTCSs). We have uncovered a highly conserved regulatory mechanism in which the output DNA-binding activity of HTCSs is suppressed by interdomain interactions in the absence of stimulating phosphorylation. A consensus amino acid motif is found to correlate with the inhibitory interaction surface while deviations from the consensus can lead to constitutive activation. Understanding of such conserved HTCS features will be important to make regulatory predictions for individual systems as well as to engineer novel systems with substitutions in the consensus to explore the glycan regulation landscape in Bacteroides.
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Affiliation(s)
- Rong Gao
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Ti Wu
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
| | - Ann M. Stock
- Center for Advanced Biotechnology and Medicine, Department of Biochemistry and Molecular Biology, Rutgers University-Robert Wood Johnson Medical School, Piscataway, New Jersey, USA
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3
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Jensen N, Maldonado-Gomez M, Krishnakumar N, Weng CY, Castillo J, Razi D, Kalanetra K, German JB, Lebrilla CB, Mills DA, Taft DH. Dietary fiber monosaccharide content alters gut microbiome composition and fermentation. Appl Environ Microbiol 2024:e0096424. [PMID: 39007602 DOI: 10.1128/aem.00964-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Members of the mammalian gut microbiota metabolize diverse complex carbohydrates that are not digested by the host, which are collectively labeled "dietary fiber." While the enzymes and transporters that each strain uses to establish a nutrient niche in the gut are often exquisitely specific, the relationship between carbohydrate structure and microbial ecology is imperfectly understood. The present study takes advantage of recent advances in complex carbohydrate structure determination to test the effects of fiber monosaccharide composition on microbial fermentation. Fifty-five fibers with varied monosaccharide composition were fermented by a pooled feline fecal inoculum in a modified MiniBioReactor array system over a period of 72 hours. The content of the monosaccharides glucose and xylose was significantly associated with the reduction of pH during fermentation, which was also predictable from the concentrations of the short-chain fatty acids lactic acid, propionic acid, and the signaling molecule indole-3-acetic acid. Microbiome diversity and composition were also predictable from monosaccharide content and SCFA concentration. In particular, the concentrations of lactic acid and propionic acid correlated with final alpha diversity and were significantly associated with the relative abundance of several of the genera, including Lactobacillus and Dubosiella. Our results suggest that monosaccharide composition offers a generalizable method to compare any dietary fiber of interest and uncover links between diet, gut microbiota, and metabolite production. IMPORTANCE The survival of a microbial species in the gut depends on the availability of the nutrients necessary for that species to survive. Carbohydrates in the form of non-host digestible fiber are of particular importance, and the set of genes possessed by each species for carbohydrate consumption can vary considerably. Here, differences in the monosaccharides that are the building blocks of fiber are considered for their impact on both the survival of different species of microbes and on the levels of microbial fermentation products produced. This work demonstrates that foods with similar monosaccharide content will have consistent effects on the survival of microbial species and on the production of microbial fermentation products.
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Affiliation(s)
- Nick Jensen
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Maria Maldonado-Gomez
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Nithya Krishnakumar
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Cheng-Yu Weng
- Department of Chemistry, University of California, Davis, California, USA
| | - Juan Castillo
- Department of Chemistry, University of California, Davis, California, USA
| | - Dale Razi
- Foods for Health Institute, University of California, Davis, California, USA
| | - Karen Kalanetra
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - J Bruce German
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Carlito B Lebrilla
- Foods for Health Institute, University of California, Davis, California, USA
- Department of Chemistry, University of California, Davis, California, USA
| | - David A Mills
- Department of Food Science and Technology, University of California, Davis, California, USA
- Foods for Health Institute, University of California, Davis, California, USA
| | - Diana H Taft
- Department of Food Science and Human Nutrition, University of Florida, Gainsville, Florida, USA
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4
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Zhang C, Pi X, Li X, Huo J, Wang W. Edible herbal source-derived polysaccharides as potential prebiotics: Composition, structure, gut microbiota regulation, and its related health effects. Food Chem 2024; 458:140267. [PMID: 38968717 DOI: 10.1016/j.foodchem.2024.140267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/13/2024] [Accepted: 06/26/2024] [Indexed: 07/07/2024]
Abstract
Recently, with changes in dietary patterns, there has been increased interest in the concept of food and medicine homology, which can help prevent disease development. This has led to a growing focus on the development of functional health foods derived from edible herbal sources. Polysaccharides, found in many edible herbal sources, are gaining popularity as natural ingredients in the production of functional food products. The gut microbiota can effectively utilize most edible herbal polysaccharides (EHPs) and produce beneficial metabolites; therefore, the prebiotic potential of EHPs is gradually being recognized. In this review, we comprehensively discuss the structural features and characterization of EHPs to promote gut microbiota regulation as well as the structure-activity relationship between EHPs and gut microbiota. As prebiotics, intestinal microbiota can use EHPs to indirectly produce metabolites such as short-chain fatty acids to promote overall health; on the other hand, different EHP structures possess some degree of selectivity on gut microbiota regulation. Moreover, we evaluate the functionality and mechanism underlying EHPs in terms of anticancer activity, antimetabolic diseases, anti-inflammatory activity, and anti-neuropsychiatric diseases.
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Affiliation(s)
- Chenxi Zhang
- Heilongjiang Academy of Chinese Medicine Science, Institute of Chinese Materia Medica, Harbin, China, 150036
| | - Xiaowen Pi
- College of Food Science, Southwest University, Chongqing, 400715, China
| | - Xiuwei Li
- Heilongjiang Academy of Chinese Medicine Science, Institute of Chinese Materia Medica, Harbin, China, 150036
| | - Jinhai Huo
- Heilongjiang Academy of Chinese Medicine Science, Institute of Chinese Materia Medica, Harbin, China, 150036.
| | - Weiming Wang
- Heilongjiang Academy of Chinese Medicine Science, Institute of Chinese Materia Medica, Harbin, China, 150036.
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5
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Murovec U, Accetto T. Transcriptomic analysis of polysaccharide utilization loci reveals substrate preferences in ruminal generalists Segatella bryantii TF1-3 and Xylanibacter ruminicola KHP1. BMC Genomics 2024; 25:495. [PMID: 38769483 PMCID: PMC11107044 DOI: 10.1186/s12864-024-10421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/15/2024] [Indexed: 05/22/2024] Open
Abstract
Bacteria of the genera Xylanibacter and Segatella are among the most dominant groups in the rumen microbiota. They are characterized by the ability to utilize different hemicelluloses and pectin of plant cell-wall as well as plant energy storage polysaccharides. The degradation is possible with the use of cell envelope bound multiprotein apparatuses coded in polysaccharide utilization loci (PULs), which have been shown to be substrate specific. The knowledge of PUL presence in rumen Xylanibacter and Segatella based on bioinformatic analyses is already established and transcriptomic and genetic approaches confirmed predicted PULs for a limited number of substrates. In this study, we transcriptomically identified additional different PULs in Xylanibacter ruminicola KHP1 and Segatella bryantii TF1-3. We also identified substrate preferences and found that specific growth rate and extent of growth impacted the choice of substrates preferentially used for degradation. These preferred substrates were used by both strains simultaneously as judged by their PUL upregulation. Lastly, β-glucan and xyloglucan were used by these strains in the absence of bioinformatically and transcriptomically identifiable PUL systems.
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Affiliation(s)
- Urška Murovec
- Department of microbiology, Biotechnical faculty, University of Ljubljana, Groblje 3, 1230, Domžale, Slovenia
| | - Tomaž Accetto
- Department of microbiology, Biotechnical faculty, University of Ljubljana, Groblje 3, 1230, Domžale, Slovenia.
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6
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Li H, Wang G, Yan X, Hu X, Li J. Effects of acetyl groups on the prebiotic properties of glucomannan extracted from Artemisia sphaerocephala Krasch seeds. Carbohydr Polym 2024; 330:121805. [PMID: 38368082 DOI: 10.1016/j.carbpol.2024.121805] [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: 10/23/2023] [Revised: 01/04/2024] [Accepted: 01/08/2024] [Indexed: 02/19/2024]
Abstract
This study explores the structural modification of glucomannan extracted from Artemisia sphaerocephala Krasch seeds (60S) to assess the impact of acetyl groups on its prebiotic characteristics. The structural changes were examined, with a focus on the degree of acetyl group substitution (DS). Both deacetylation and acetylation had limited influence on the molecular properties of 60S. Despite these modifications, the apparent viscosity of all samples remained consistently low. In vitro fermentation experiments revealed that Escherichia-Shigella decreased as DS increased, while Bacteroides ovatus was enriched. Acetylation had no significant impact on the utilization rate of 60S but led to a reduction in the production of propionic acid. Furthermore, untargeted metabolomics analysis confirmed the changes in propionic acid levels. Notably, metabolites such as N-acetyl-L-tyrosine, γ-muricholic acid, and taurocholate were upregulated by acetylated derivatives. Overall, acetyl groups are speculated to play a pivotal role in the prebiotic properties of 60S.
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Affiliation(s)
- Haocheng Li
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Gongda Wang
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Ximei Yan
- College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an 710119, Shaanxi, China.
| | - Junjun Li
- College of Enology, Northwest A&F University, Yangling 712100, Shaanxi, China.
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7
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Zhang X, Yi X, Yu W, Chen T, Gao B, Gilbert RG, Li C. Subtle structural variations of resistant starch from whole cooked rice significantly impact metabolic outputs of gut microbiota. Carbohydr Polym 2024; 329:121779. [PMID: 38286529 DOI: 10.1016/j.carbpol.2024.121779] [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: 09/14/2023] [Revised: 12/12/2023] [Accepted: 01/01/2024] [Indexed: 01/31/2024]
Abstract
While cooked rice is widely consumed as a whole food, the specific characteristics and impact of its resistant starch (RS) on gut microbiota are largely unexplored. In this study, three rice varieties with distinct starch molecular structures were used to prepare RS from cooked rice. All three types of RS had a crystalline structure characterized as B + V type, with the V type being the predominant crystalline polymorph. Distinct differences in chain-length distributions were observed among different RSs, with rapidly fermentable starch fractions comprising short amylopectin and long amylose chains, while the degrees of polymerization (DPs) ∼ 10, 37, 65, and 105 fractions comprised the slowly fermentable starch. Jasmine rice RS showed the highest proportion of this slowly fermentable starch fraction, which appeared to be specifically utilized by Megasphaera_elsdenii_DSM_20460 OTU198. The fermentation of Jasmine RS resulted in the highest production of butyrate after 24 h, which was positively correlated with the relative abundance of Megasphaera_elsdenii_DSM_20460 OTU198. These findings collectively indicate that RS in cooked rice with a higher V type crystallinity and DPs ∼ 10, 37, 65, and 105 fractions promote butyrate production and stimulate the growth of butyrate-producing bacteria in the human gut, thereby conferring beneficial effects on gut health.
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Affiliation(s)
- Xiaowei Zhang
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China; Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xueer Yi
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Wenwen Yu
- Department of Food Science & Engineering, Jinan University, Huangpu West Avenue 601, Guangzhou City 510632, China
| | - Tingting Chen
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Boyan Gao
- Department of Food Science and Engineering, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Robert G Gilbert
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology, College of Agriculture, Yangzhou University, Yangzhou 225009, Jiangsu Province, China; The University of Queensland, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, Brisbane, QLD 4072, Australia
| | - Cheng Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China.
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8
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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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9
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Gerrick ER, Zlitni S, West PT, Carter MM, Mechler CM, Olm MR, Caffrey EB, Li JA, Higginbottom SK, Severyn CJ, Kracke F, Spormann AM, Sonnenburg JL, Bhatt AS, Howitt MR. Metabolic diversity in commensal protists regulates intestinal immunity and trans-kingdom competition. Cell 2024; 187:62-78.e20. [PMID: 38096822 DOI: 10.1016/j.cell.2023.11.018] [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: 08/26/2022] [Revised: 08/01/2023] [Accepted: 11/14/2023] [Indexed: 01/05/2024]
Abstract
The microbiota influences intestinal health and physiology, yet the contributions of commensal protists to the gut environment have been largely overlooked. Here, we discover human- and rodent-associated parabasalid protists, revealing substantial diversity and prevalence in nonindustrialized human populations. Genomic and metabolomic analyses of murine parabasalids from the genus Tritrichomonas revealed species-level differences in excretion of the metabolite succinate, which results in distinct small intestinal immune responses. Metabolic differences between Tritrichomonas species also determine their ecological niche within the microbiota. By manipulating dietary fibers and developing in vitro protist culture, we show that different Tritrichomonas species prefer dietary polysaccharides or mucus glycans. These polysaccharide preferences drive trans-kingdom competition with specific commensal bacteria, which affects intestinal immunity in a diet-dependent manner. Our findings reveal unappreciated diversity in commensal parabasalids, elucidate differences in commensal protist metabolism, and suggest how dietary interventions could regulate their impact on gut health.
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Affiliation(s)
- Elias R Gerrick
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Patrick T West
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew M Carter
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Claire M Mechler
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew R Olm
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elisa B Caffrey
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jessica A Li
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven K Higginbottom
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Christopher J Severyn
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Division of Hematology/Oncology/Stem Cell Transplant and Regenerative Medicine Stanford University, Palo Alto, CA 94305, USA
| | - Frauke Kracke
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA
| | - Alfred M Spormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305, USA; Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Justin L Sonnenburg
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael R Howitt
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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10
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Xu H, Pudlo NA, Cantu-Jungles TM, Tuncil YE, Nie X, Kaur A, Reuhs BL, Martens EC, Hamaker BR. When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures. ISME COMMUNICATIONS 2024; 4:ycae037. [PMID: 38645272 PMCID: PMC11032216 DOI: 10.1093/ismeco/ycae037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/04/2024] [Accepted: 03/18/2024] [Indexed: 04/23/2024]
Abstract
Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight Bacteroides xylan-degrading strains. For example, Bacteroides cellulosilyticus DSM 14838 (Bacteroides cellulosilyticus) grew well on an array of complex and simple structures, while Bacteroides ovatus 3-1-23 grew well only on the simple structures. In a competition experiment, B. cellulosilyticus growth was favored over B. ovatus on the complex AX-based structure. On the other hand, on the simple structure, B. ovatus strongly outcompeted B. cellulosilyticus, which was eliminated from the competitive environment by Day 11. This adaptation to fine structure and resulting competition dynamics indicate that dietary fiber chemical structures, whether complex or simple, favor certain gut bacteria. Overall, this work supports a concept that fiber degraders diversify their competitive abilities to access substrates across the spectrum of heterogeneity of fine structural features of dietary fibers.
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Affiliation(s)
- Haidi Xu
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
- Present address: Nestlé Health Science, Shanghai, P.R. China
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, Medical Sciences Research Building II, 1150 W Medical Center Dr., University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Thaisa M Cantu-Jungles
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Yunus E Tuncil
- Food Engineering Department, Yeni Meram Boulevard Kasım Halife Street, Necmettin Erbakan University, Konya 42090, Turkey
| | - Xin Nie
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Amandeep Kaur
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Bradley L Reuhs
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
| | - Eric C Martens
- Department of Microbiology and Immunology, Medical Sciences Research Building II, 1150 W Medical Center Dr., University of Michigan Medical School, Ann Arbor, MI 48109, United States
| | - Bruce R Hamaker
- Whistler Center for Carbohydrate Research, Department of Food Science, 745 Agriculture Mall Drive, Purdue University, West Lafayette, IN 47907, United States
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11
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Duan H, Yu Q, Ni Y, Li J, Yu L, Fan L. Interactions between wheat germ polysaccharide and gut microbiota through in vitro batch fecal fermentation and an aging mice model: Targeting enrichment of Bacteroides uniformis and Bifidobacterium pseudocatenulatum. Int J Biol Macromol 2023; 253:127559. [PMID: 37865367 DOI: 10.1016/j.ijbiomac.2023.127559] [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: 08/04/2023] [Revised: 09/23/2023] [Accepted: 10/18/2023] [Indexed: 10/23/2023]
Abstract
The interaction between wheat germ polysaccharide (WGP) and gut microbiota remains relatively less investigated. Thus, this study explored their interaction via in vitro batch fecal fermentation. WGP elevated dramatically the relative abundances of Bacteroides (especially Ba. xylanisolvens, Ba. uniformis, and Ba. intestinalis), Bifidobacterium (especially Bi. pseudocatenulatum) and Eubacterium, and decreased Alistipes, Klebsiella, Bilophila and Sutterella. Moreover, the metabolomics and Spearman correlation results showed that these alterations in gut microbiota gave rise to over 13-fold augmentation in the quantities of short-chain fatty acids (SCFAs) and indole-3-lactic acid, as well as 7.17- and 4.23-fold increase in acetylcholine and GABA, respectively, at 24 h of fermentation. Interestingly, PICRUSt analysis showed that WGP markedly reduced aging pathway, and enriched nervous system pathway. Therefore, the D-gal-induced aging mice model was used to further verify these effects. The results demonstrated that WGP had a protective effect on D-gal-induced behavioral deficits, particularly in locomotor activity, and spatial and recognition memory. WGP elevated dramatically the relative abundances of Bacteroides (especially Ba. sartorii and Ba. uniformis), Bifidobacterium (especially Bi. pseudocatenulatum) and Parabacteroides, and decreased Alistipes and Candidatus Arthromitus. These findings highlight the potential utility of WGP as a dietary supplement for retarding the aging process and mitigating age-associated learning and memory decline via the targeted enrichment of Bacteroides and Bifidobacterium and the related metabolites.
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Affiliation(s)
- Hui Duan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qun Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yang Ni
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jinwei Li
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.
| | - Liuping Fan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China.
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12
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Njoku EN, Mottawea W, Hassan H, Gomaa A, Bordenave N, Hammami R. Bioengineered Wheat Arabinoxylan - Fostering Next-Generation Prebiotics Targeting Health-Related Gut Microbes. PLANT FOODS FOR HUMAN NUTRITION (DORDRECHT, NETHERLANDS) 2023; 78:698-703. [PMID: 37919537 DOI: 10.1007/s11130-023-01120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Dietary prebiotic fibers play an important role in modulating gut microbiota by enhancing the abundance of beneficial microorganisms and their bioactive metabolites. However, dietary fibers are a structurally heterogeneous class of polysaccharides, varying in molar mass, branching patterns, and monosaccharide composition, which could influence their utilization by various gut microorganisms. The present study aimed to investigate the effects of molar mass and chemical structure of wheat arabinoxylan fiber (AX) on the growth and metabolism of two key gut resident bacteria (Faecalibacterium prausnitzii and Lacticaseibacillus rhamnosus LGG), which are linked to human health. For this purpose, low, medium, and high molar masses of AX (LAX, MAX, and HAX, respectively) were modified with specific α-arabinofuranosidases to leave only singly substituted, only doubly substituted, or unsubstituted xylose units. Almost all the modified AX samples showed a better prebiotic score than unmodified AX for different molar masses. The modified LAX exhibited a better prebiotic effect than HAX and MAX. In addition, LAX, with doubly substituted xylose units, exhibited the highest prebiotic potential and SCFA production by both microorganisms. Furthermore, AX, either singly or doubly substituted, had a consistent impact on L. rhamnosus growth, whereas AX, with all arabinose residues removed, had a greater impact on F. prausnitzii. These findings support the potential of bioengineered AX as next-generation prebiotics targeting health-related gut microbes.
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Affiliation(s)
- Emmanuel N Njoku
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Walid Mottawea
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Hebatoallah Hassan
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Ahmed Gomaa
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- National Research Center, Nutrition and Food Science Department, Cairo, Egypt
| | - Nicolas Bordenave
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Chemistry and Biomolecular Sciences, Faculty of Sciences, University of Ottawa, Ottawa, Ontario, Canada
| | - Riadh Hammami
- NuGut Research Platform, School of Nutrition Sciences, Faculty of Health Sciences, University of Ottawa, Ottawa, Ontario, Canada.
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada.
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13
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Cantu-Jungles TM, Hamaker BR. Tuning Expectations to Reality: Don't Expect Increased Gut Microbiota Diversity with Dietary Fiber. J Nutr 2023; 153:3156-3163. [PMID: 37690780 DOI: 10.1016/j.tjnut.2023.09.001] [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: 08/01/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023] Open
Abstract
Dietary approaches, particularly those including fiber supplementation, can be used to promote health benefits by shaping gut microbial communities. Whereas community diversity measures, such as richness and evenness, are often used in microbial ecology to make sense of these complex and vast microbial ecosystems, it is less clear how these concepts apply when dietary fiber supplementation is given. In this perspective, we summarize and demonstrate how factors including experimental approach, number of bacteria sharing a dietary fiber, and initial relative abundances of bacteria that use a fiber can significantly affect diversity outcomes in fiber fermentation studies. We also show that a reduction in alpha diversity is possible, and perhaps expected, for most approaches that use fermentable fibers to beneficially shape the gut microbial community while still achieving health-related improvements.
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Affiliation(s)
- Thaisa M Cantu-Jungles
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States.
| | - Bruce R Hamaker
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, United States
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14
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Mansoor AER, O'Neil CA, Kwon JH. The role of microbiome-based therapeutics for the reduction and prevention of antimicrobial-resistant organism colonization. Anaerobe 2023; 83:102772. [PMID: 37572864 DOI: 10.1016/j.anaerobe.2023.102772] [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: 05/31/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/14/2023]
Abstract
The gut is host to a diverse array of microbiota that constitute a complex ecological system crucial to human physiology. Disruptors to the normal host microbiota, such as antimicrobials, can cause a loss of species diversity in the gut, reducing its ability to resist colonization by invading pathogens and potentially leading to colonization with antimicrobial resistant organisms (AROs). ARO negatively impact gut health by disrupting the usual heterogeneity of gut microbiota and have the potential to cause systemic disease. In recent years, fecal microbiota transplantation (FMT) has been increasingly explored in the management of specific disease states such as Clostridioides difficile infection (CDI). Promising data from management of CDI has led to considerable interest in understanding the role of therapeutics to restore the gut microbiota to a healthy state. This review aims to discuss key studies that highlight the current landscape, and explore existing clinical evidence, for the use of FMT and microbiome-based therapeutics in combating intestinal colonization with ARO. We also explore potential future directions of such therapeutics and discuss unaddressed needs in this field that merit further investigation.
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Affiliation(s)
- Armaghan-E-Rehman Mansoor
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, 4523 Clayton Avenue, St. Louis, MO, 63110, USA.
| | - Caroline A O'Neil
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, 4523 Clayton Avenue, St. Louis, MO, 63110, USA.
| | - Jennie H Kwon
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, 4523 Clayton Avenue, St. Louis, MO, 63110, USA.
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15
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Beller ZW, Wesener DA, Seebeck TR, Guruge JL, Byrne AE, Henrissat S, Terrapon N, Henrissat B, Rodionov DA, Osterman AL, Suarez C, Bacalzo NP, Chen Y, Couture G, Lebrilla CB, Zhang Z, Eastlund ER, McCann CH, Davis GD, Gordon JI. Inducible CRISPR-targeted "knockdown" of human gut Bacteroides in gnotobiotic mice discloses glycan utilization strategies. Proc Natl Acad Sci U S A 2023; 120:e2311422120. [PMID: 37733741 PMCID: PMC10523453 DOI: 10.1073/pnas.2311422120] [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: 07/10/2023] [Accepted: 08/08/2023] [Indexed: 09/23/2023] Open
Abstract
Understanding how members of the human gut microbiota prioritize nutrient resources is one component of a larger effort to decipher the mechanisms defining microbial community robustness and resiliency in health and disease. This knowledge is foundational for development of microbiota-directed therapeutics. To model how bacteria prioritize glycans in the gut, germfree mice were colonized with 13 human gut bacterial strains, including seven saccharolytic Bacteroidaceae species. Animals were fed a Western diet supplemented with pea fiber. After community assembly, an inducible CRISPR-based system was used to selectively and temporarily reduce the absolute abundance of Bacteroides thetaiotaomicron or B. cellulosilyticus by 10- to 60-fold. Each knockdown resulted in specific, reproducible increases in the abundances of other Bacteroidaceae and dynamic alterations in their expression of genes involved in glycan utilization. Emergence of these "alternate consumers" was associated with preservation of community saccharolytic activity. Using an inducible system for CRISPR base editing in vitro, we disrupted translation of transporters critical for utilizing dietary polysaccharides in Phocaeicola vulgatus, a B. cellulosilyticus knockdown-responsive taxon. In vitro and in vivo tests of the resulting P. vulgatus mutants allowed us to further characterize mechanisms associated with its increased fitness after knockdown. In principle, the approach described can be applied to study utilization of a range of nutrients and to preclinical efforts designed to develop therapeutic strategies for precision manipulation of microbial communities.
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Affiliation(s)
- Zachary W. Beller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Darryl A. Wesener
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Timothy R. Seebeck
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Janaki L. Guruge
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Alexandra E. Byrne
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
| | - Suzanne Henrissat
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille University, 13288Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. LyngbyDK-2800, Denmark
- Department of Biological Sciences, King Abdulaziz University, Jeddah21589, Saudi Arabia
| | - Dmitry A. Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Andrei L. Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA92037
| | - Chris Suarez
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Ye Chen
- Department of Chemistry, University of California, Davis, CA95616
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA95616
| | | | - Zhigang Zhang
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Erik R. Eastlund
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Caitlin H. McCann
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Gregory D. Davis
- Genome Engineering R&D, MilliporeSigma, the Life Science business Merck KGaA, Darmstadt, Germany, St. Louis, MO63103
| | - Jeffrey I. Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO63110
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St. Louis, MO63110
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16
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Xu Y, Wang F, Mi K, Wang X, Wang D, Zhao Q, Wang J, Liu Z, Zhang Q, Liu Y, Zhang X, Liu X. Biglycan regulated colorectal cancer progress by modulating enteric neuron-derived IL-10 and abundance of Bacteroides thetaiotaomicron. iScience 2023; 26:107515. [PMID: 37664615 PMCID: PMC10469580 DOI: 10.1016/j.isci.2023.107515] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/01/2022] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
Biglycan (BGN) is a proteoglycan with branch chains and highly expressed in enteric neurons in the tumor tissue of colorectal cancer (CRC), which is negatively associated with survival rates in patients with CRC. However, how the proteoglycan promotes the progress of CRC through interacting with bacteria and regulating the immune response of enteric neurons remains largely unknown. In the present study, we found that biglycan deficiency changed tumor distribution in a colitis-associated colon cancer model. Furthermore, we revealed that BGN deficiency inhibits tumor growth in an allograft tumor model and the migration of cancer cell by upregulating interleukin-10 expression in enteric neurons. Significantly, we demonstrated that biglycan deficiency enriched the abundance of Bacteroides thetaiotaomicron through competing with it for chondroitin sulfate to inhibit CRC progress. Our work provided new insights into the interaction between host proteoglycan and gut microbiota as well as the role of enteric neurons in the tumor microenvironment.
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Affiliation(s)
- Yuyu Xu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Fei Wang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
- The Affiliated Mental Health Center of Jiangnan University, Wuxi Central Rehabilitation Hospital, Wuxi, Jiangsu 214151, China
| | - Kai Mi
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xinyuan Wang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Danlei Wang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Qing Zhao
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Jingjing Wang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Zhi Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Qingqing Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Yang Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xuemei Zhang
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
| | - Xingyin Liu
- Department of Pathogen Biology-Microbiology Division, State Key Laboratory of Reproductive Medicine and Offspring Health, Key Laboratory of Pathogen of Jiangsu Province, Key Laboratory of Human Functional Genomics of Jiangsu Province, Center of Global Health, Nanjing Medical University, Nanjing 211166, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
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17
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Takano S, Vila JCC, Miyazaki R, Sánchez Á, Bajić D. The Architecture of Metabolic Networks Constrains the Evolution of Microbial Resource Hierarchies. Mol Biol Evol 2023; 40:msad187. [PMID: 37619982 PMCID: PMC10476156 DOI: 10.1093/molbev/msad187] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/18/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
Microbial strategies for resource use are an essential determinant of their fitness in complex habitats. When facing environments with multiple nutrients, microbes often use them sequentially according to a preference hierarchy, resulting in well-known patterns of diauxic growth. In theory, the evolutionary diversification of metabolic hierarchies could represent a mechanism supporting coexistence and biodiversity by enabling temporal segregation of niches. Despite this ecologically critical role, the extent to which substrate preference hierarchies can evolve and diversify remains largely unexplored. Here, we used genome-scale metabolic modeling to systematically explore the evolution of metabolic hierarchies across a vast space of metabolic network genotypes. We find that only a limited number of metabolic hierarchies can readily evolve, corresponding to the most commonly observed hierarchies in genome-derived models. We further show how the evolution of novel hierarchies is constrained by the architecture of central metabolism, which determines both the propensity to change ranks between pairs of substrates and the effect of specific reactions on hierarchy evolution. Our analysis sheds light on the genetic and mechanistic determinants of microbial metabolic hierarchies, opening new research avenues to understand their evolution, evolvability, and ecology.
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Affiliation(s)
- Sotaro Takano
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Jean C C Vila
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ryo Miyazaki
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Computational Bio Big Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo, Japan
| | - Álvaro Sánchez
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Department of Microbial Biotechnology, CNB-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Djordje Bajić
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
- Section of Industrial Microbiology, Department of Biotechnology, Technical University Delft, Delft, The Netherlands
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18
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Wang Z, Wang S, Xu Q, Kong Q, Li F, Lu L, Xu Y, Wei Y. Synthesis and Functions of Resistant Starch. Adv Nutr 2023; 14:1131-1144. [PMID: 37276960 PMCID: PMC10509415 DOI: 10.1016/j.advnut.2023.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/15/2023] [Accepted: 06/01/2023] [Indexed: 06/07/2023] Open
Abstract
Resistant starch (RS) has become a popular topic of research in recent years. Most scholars believe that there are 5 types of RS. However, accumulating evidence indicates that in addition to starch-lipid complexes, which are the fifth type of RS, complexes containing starch and other substances can also be generated. The physicochemical properties and physiologic functions of these complexes are worth exploring. New physiologic functions of several original RSs are constantly being discovered. Research shows that RS can provide health improvements in many patients with chronic diseases, including diabetes and obesity, and even has potential benefits for kidney disease and colorectal cancer. Moreover, RS can alter the short-chain fatty acids and microorganisms in the gut, positively regulating the body's internal environment. Despite the increase in its market demand, RS production remains limited. Upscaling RS production is thus an urgent requirement. This paper provides detailed insights into the classification, synthesis, and efficacy of RS, serving as a starting point for the future development and applications of RS based on the current status quo.
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Affiliation(s)
- Zhanggui Wang
- Department of Radiotherapy, Anhui No. 2 Provincial People's Hospital, Hefei, China
| | - Shuli Wang
- Department of Radiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qinhong Xu
- Department of Acupuncture and Massage, Anhui No.2 Provincial People's Hospital, Hefei, China
| | - Qi Kong
- Department of Radiotherapy, Anhui No. 2 Provincial People's Hospital, Hefei, China
| | - Fei Li
- Department of Radiotherapy, Anhui No. 2 Provincial People's Hospital, Hefei, China
| | - Lin Lu
- Department of Radiotherapy, Anhui No. 2 Provincial People's Hospital, Hefei, China
| | - Yibiao Xu
- Department of Neurosurgery, The Fifth People's Hospital of Huai 'an, Huai' an, China
| | - Yali Wei
- Department of Radiotherapy, Anhui No. 2 Provincial People's Hospital, Hefei, China; Department of Women's Health, Jiaxing Maternity and Child Health Care Hospital, Affiliated Women and Children's Hospital of Jiaxing University, Jiaxing, China.
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19
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Wang X, Li X, Zhang L, An L, Guo L, Huang L, Gao W. Recent progress in plant-derived polysaccharides with prebiotic potential for intestinal health by targeting gut microbiota: a review. Crit Rev Food Sci Nutr 2023:1-30. [PMID: 37651130 DOI: 10.1080/10408398.2023.2248631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Natural products of plant origin are of high interest and widely used, especially in the food industry, due to their low toxicity and wide range of bioactive properties. Compared to other plant components, the safety of polysaccharides has been generally recognized. As dietary fibers, plant-derived polysaccharides are mostly degraded in the intestine by polysaccharide-degrading enzymes secreted by gut microbiota, and have potential prebiotic activity in both non-disease and disease states, which should not be overlooked, especially in terms of their involvement in the treatment of intestinal diseases and the promotion of intestinal health. This review elucidates the regulatory effects of plant-derived polysaccharides on gut microbiota and summarizes the mechanisms involved in targeting gut microbiota for the treatment of intestinal diseases. Further, the structure-activity relationships between different structural types of plant-derived polysaccharides and the occurrence of their prebiotic activity are further explored. Finally, the practical applications of plant-derived polysaccharides in food production and food packaging are summarized and discussed, providing important references for expanding the application of plant-derived polysaccharides in the food industry or developing functional dietary supplements.
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Affiliation(s)
- Xiaozhen Wang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Xia Li
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Luyao Zhang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Lingzhuo An
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, Academy of Chinese Medical Sciences, Beijing, China
| | - Wenyuan Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, China
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20
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Yip AYG, King OG, Omelchenko O, Kurkimat S, Horrocks V, Mostyn P, Danckert N, Ghani R, Satta G, Jauneikaite E, Davies FJ, Clarke TB, Mullish BH, Marchesi JR, McDonald JAK. Antibiotics promote intestinal growth of carbapenem-resistant Enterobacteriaceae by enriching nutrients and depleting microbial metabolites. Nat Commun 2023; 14:5094. [PMID: 37607936 PMCID: PMC10444851 DOI: 10.1038/s41467-023-40872-z] [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: 05/22/2023] [Accepted: 08/11/2023] [Indexed: 08/24/2023] Open
Abstract
The intestine is the primary colonisation site for carbapenem-resistant Enterobacteriaceae (CRE) and serves as a reservoir of CRE that cause invasive infections (e.g. bloodstream infections). Broad-spectrum antibiotics disrupt colonisation resistance mediated by the gut microbiota, promoting the expansion of CRE within the intestine. Here, we show that antibiotic-induced reduction of gut microbial populations leads to an enrichment of nutrients and depletion of inhibitory metabolites, which enhances CRE growth. Antibiotics decrease the abundance of gut commensals (including Bifidobacteriaceae and Bacteroidales) in ex vivo cultures of human faecal microbiota; this is accompanied by depletion of microbial metabolites and enrichment of nutrients. We measure the nutrient utilisation abilities, nutrient preferences, and metabolite inhibition susceptibilities of several CRE strains. We find that CRE can use the nutrients (enriched after antibiotic treatment) as carbon and nitrogen sources for growth. These nutrients also increase in faeces from antibiotic-treated mice and decrease following intestinal colonisation with carbapenem-resistant Escherichia coli. Furthermore, certain microbial metabolites (depleted upon antibiotic treatment) inhibit CRE growth. Our results show that killing gut commensals with antibiotics facilitates CRE colonisation by enriching nutrients and depleting inhibitory microbial metabolites.
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Affiliation(s)
- Alexander Y G Yip
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Olivia G King
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Oleksii Omelchenko
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sanjana Kurkimat
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Victoria Horrocks
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Phoebe Mostyn
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Nathan Danckert
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Rohma Ghani
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Department of Infectious Disease, Imperial College Healthcare NHS Trust, London, UK
| | - Giovanni Satta
- UCL Centre for Clinical Microbiology, University College London, London, UK
| | - Elita Jauneikaite
- NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, Department of Infectious Disease, Imperial College London, London, UK
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Frances J Davies
- Department of Infectious Disease, Imperial College Healthcare NHS Trust, London, UK
| | - Thomas B Clarke
- Centre for Bacterial Resistance Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - Benjamin H Mullish
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
- Departments of Gastroenterology and Hepatology, St Mary's Hospital, Imperial College Healthcare NHS Trust, Paddington, London, UK
| | - Julian R Marchesi
- Division of Digestive Diseases, Department of Metabolism, Digestion and Reproduction, Faculty of Medicine, St Mary's Hospital Campus, Imperial College London, London, UK
| | - Julie A K McDonald
- Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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21
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Brown HA, DeVeaux AL, Juliano BR, Photenhauer AL, Boulinguiez M, Bornschein RE, Wawrzak Z, Ruotolo BT, Terrapon N, Koropatkin NM. BoGH13A Sus from Bacteroides ovatus represents a novel α-amylase used for Bacteroides starch breakdown in the human gut. Cell Mol Life Sci 2023; 80:232. [PMID: 37500984 PMCID: PMC10540511 DOI: 10.1007/s00018-023-04812-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 07/29/2023]
Abstract
Members of the Bacteroidetes phylum in the human colon deploy an extensive number of proteins to capture and degrade polysaccharides. Operons devoted to glycan breakdown and uptake are termed polysaccharide utilization loci or PUL. The starch utilization system (Sus) is one such PUL and was initially described in Bacteroides thetaiotaomicron (Bt). BtSus is highly conserved across many species, except for its extracellular α-amylase, SusG. In this work, we show that the Bacteroides ovatus (Bo) extracellular α-amylase, BoGH13ASus, is distinguished from SusG in its evolutionary origin and its domain architecture and by being the most prevalent form in Bacteroidetes Sus. BoGH13ASus is the founding member of both a novel subfamily in the glycoside hydrolase family 13, GH13_47, and a novel carbohydrate-binding module, CBM98. The BoGH13ASus CBM98-CBM48-GH13_47 architecture differs from the CBM58 embedded within the GH13_36 of SusG. These domains adopt a distinct spatial orientation and invoke a different association with the outer membrane. The BoCBM98 binding site is required for Bo growth on polysaccharides and optimal enzymatic degradation thereof. Finally, the BoGH13ASus structure features bound Ca2+ and Mn2+ ions, the latter of which is novel for an α-amylase. Little is known about the impact of Mn2+ on gut bacterial function, much less on polysaccharide consumption, but Mn2+ addition to Bt expressing BoGH13ASus specifically enhances growth on starch. Further understanding of bacterial starch degradation signatures will enable more tailored prebiotic and pharmaceutical approaches that increase starch flux to the gut.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Anna L DeVeaux
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Brock R Juliano
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amanda L Photenhauer
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Matthieu Boulinguiez
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | | | - Zdzislaw Wawrzak
- Synchrotron Research Center, Life Science Collaborative Access Team, Northwestern University, Lemont, IL, USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, UMR 7257, CNRS AMU; USC1408 INRAE, 13288, Marseille, France
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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22
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Cao C, Wang L, Zhang X, Ai C, Wang Z, Huang L, Song S, Zhu B. Interaction between Bacteroidetes species in the fermentation of Lycium barbarum arabinogalactan. Food Chem 2023; 409:135288. [PMID: 36584527 DOI: 10.1016/j.foodchem.2022.135288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 10/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
The present study investigated the utilization of an arabinogalactan from Lycium barbarum (LBP-3) by intestinal Bacteroidetes species. The mixed-culture assay showed 58.4 % LBP-3 was utilized, and Bacteroides caccae and Phocaeicola vulgatus utilized more LBP-3 in single-culture compared to others. During in vitro fermentation of LBP-3, P. vulgatus favored arabinose while B. caccae preferred galactose. Moreover, 9 and 25 oligosaccharides were identified by HPLC-MSn in conditioned media (CM) derived from B. caccae and P. vulgatus, respectively. All of 3 tested Parabacteroides species (P. distasonis, P. goldsteinii, and P. johnsonii) markedly proliferated in CM of B. caccae and P. vulgatus, and proliferations of B. uniformis, B. finegoldii, B. ovatus and B. thetaiotaomicron also increased significantly in CM of B. caccae. The study suggests that the ability of Bacteroidetes species to degrade LBP-3 and sheds light on cooperative interactions of Bacteroides, Phocaeicola, and Parabacteroides species in the presence of LBP-3.
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Affiliation(s)
- Cui Cao
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China; Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, PR China
| | - Lilong Wang
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China
| | - Xueqian Zhang
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China; Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, PR China
| | - Chunqing Ai
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China
| | - Zhongfu Wang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, PR China
| | - Linjuan Huang
- Shaanxi Natural Carbohydrate Resource Engineering Research Center, College of Food Science and Technology, Northwest University, Xi'an 710069, PR China.
| | - Shuang Song
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China.
| | - Beiwei Zhu
- Collaborative Innovation Center of Seafood Deep Processing, National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, PR China; National & Local Joint Engineering Laboratory for Marine Bioactive Polysaccharide Development and Application, Dalian Polytechnic University, Dalian 116034, PR China
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23
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Tang N, Zhang C, Ma K, Wang X, Xiao L, Zhang X, Rui X, Li W. Advanced structural characterization and in vitro fermentation prebiotic properties of cell wall polysaccharide from Kluyveromyces marxianus. Int J Biol Macromol 2023; 241:124420. [PMID: 37085078 DOI: 10.1016/j.ijbiomac.2023.124420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/26/2023] [Accepted: 04/08/2023] [Indexed: 04/23/2023]
Abstract
Through previous study, the three yeast α-mannans (MPS) from various sources of Kluyveromyces marxianus (LZ-MPS, MC-MPS, and G-MPS) were preliminarily characterized. In this study, the advanced structural characterization and the in vitro human fecal fermentation behavior of the three MPS were investigated. According to the results of this study, the polysaccharide molecules of the three MPS were aggregated in solution, supporting their branched chain structure. After in vitro fermentation, the molecular weight and pH of fermentation broth decreased significantly, indicating that the three MPS could be utilized by human gut microbiota. Meanwhile, the production of total short-chain fatty acids (SCFAs) of the three MPS was promoted, especially the production of propionic acid was 45.55, 38.23, and 38.87 mM, respectively. In particular, the three MPS have the ability to alter the composition of human gut microbiota, especially to promote the proliferation of Bacteroidetes, suggesting that the bioactivities of the three MPS can be significantly influenced by intestine Bacteroidetes. In terms of metabolism, all MPS can promote cofactors, vitamins, amino acid metabolism, and glycan biosynthesis and metabolism of bacteria. In consequence, the three MPS were confirmed to regulate the human gut microbiota, increase the level of SCFAs, promote the metabolisms of bacteria on amino acid and glycan, and improve the intestinal health.
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Affiliation(s)
- Nanyu Tang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Changliang Zhang
- Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu 214400, PR China; Probiotics Australia Pty, Ormeau, Queensland 4208, Australia
| | - Kai Ma
- Jiangsu Biodep Biotechnology Co., Ltd., Jiangyin, Jiangsu 214400, PR China; Probiotics Australia Pty, Ormeau, Queensland 4208, Australia
| | - Xiaomeng Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Luyao Xiao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xueliang Zhang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xin Rui
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Wei Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China.
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24
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Effect of Agaricus bisporus Polysaccharides on Human Gut Microbiota during In Vitro Fermentation: An Integrative Analysis of Microbiome and Metabolome. Foods 2023; 12:foods12040859. [PMID: 36832934 PMCID: PMC9957339 DOI: 10.3390/foods12040859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/05/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Agaricus bisporus polysaccharide (ABP) is an important active component in edible mushrooms, but its interaction with gut microbiota is unclear. Therefore, this study evaluated the effect of ABP on the composition and metabolites of human gut microbiota by in vitro batch fermentation. The main degrading bacteria for ABP were Bacteroides, Streptococcus, Enterococcus, Paraprevotella, Bifidobacterium, Lactococcus, Megamonas, and Eubacterium, whose relative abundances increased during 24 h of in vitro fermentation. The short-chain fatty acids (SCFAs) content also increased more than 15-fold, accordingly. Moreover, the effects of ABP on the relative abundance of Bacteroides (Ba.) and Bifidobacterium (Bi.) at the species level were further determined. ABP can enrich Ba. thetaiotaomicron, Ba. intestinalis, Ba. uniformis, and Bi. longum. PICRUSt analysis revealed that the catabolism of ABP was accompanied by changes in the metabolism of carbohydrates, nucleotides, lipids and amino acids, which were also supported by metabonomic results. It is worth mentioning that, after 24 h fermentation, the relative amounts of gamma-aminobutyric acid (GABA), nicotinamide and nicotinamide adenine dinucleotide (NAD+) had 14.43-, 11.34- and 15.36-fold increases, respectively, which were positively related to Bacteroides (Ba. thetaiotaomicron, Ba. intestinalis), Streptococcus, and Bi. longum (|r| > 0.98). These results laid the research foundation for exploring ABP as a potential prebiotic or dietary supplement for the targeted regulation of gut microbiota or metabolites.
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25
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Modesto JL, Pearce VH, Townsend GE. Harnessing gut microbes for glycan detection and quantification. Nat Commun 2023; 14:275. [PMID: 36650134 PMCID: PMC9845299 DOI: 10.1038/s41467-022-35626-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 12/13/2022] [Indexed: 01/19/2023] Open
Abstract
Glycans facilitate critical biological functions and control the mammalian gut microbiota composition by supplying differentially accessible nutrients to distinct microbial subsets. Therefore, identifying unique glycan substrates that support defined microbial populations could inform therapeutic avenues to treat diseases via modulation of the gut microbiota composition and metabolism. However, examining heterogeneous glycan mixtures for individual microbial substrates is hindered by glycan structural complexity and diversity, which presents substantial challenges to glycomics approaches. Fortuitously, gut microbes encode specialized sensor proteins that recognize unique glycan structures and in-turn activate predictable, specific, and dynamic transcriptional responses. Here, we harness this microbial machinery to indicate the presence and abundance of compositionally similar, yet structurally distinct glycans, using a transcriptional reporter we develop. We implement these tools to examine glycan mixtures, isolate target molecules for downstream characterization, and quantify the recovered products. We assert that this toolkit could dramatically enhance our understanding of the mammalian intestinal environment and identify host-microbial interactions critical for human health.
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Affiliation(s)
- Jennifer L Modesto
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA.,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA
| | - Victoria H Pearce
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA.,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA.,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA
| | - Guy E Townsend
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033, USA. .,Penn State Microbiome Center, The Pennsylvania State University, State College, PA, 16802, USA. .,Center for Molecular Carcinogenesis and Toxicology, The Pennsylvania State University, State College, PA, 16802, USA.
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26
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Tao R, Lu K, Zong G, Xia Y, Han H, Zhao Y, Wei Z, Lu Y. Ginseng polysaccharides: Potential antitumor agents. J Ginseng Res 2023; 47:9-22. [PMID: 36644386 PMCID: PMC9834022 DOI: 10.1016/j.jgr.2022.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/18/2022] [Accepted: 07/11/2022] [Indexed: 01/18/2023] Open
Abstract
As a famous herbal medicine in China and Asia, ginseng (Panax ginseng C. A. Meyer) is also known as the "King of All Herbs" and has long been used in medicine and healthcare. In addition to the obvious biological activities of ginsenosides, ginseng polysaccharides (GPs) exhibit excellent antitumor, antioxidant stress, and immunomodulatory effects. In particular, GPs can exert an antitumor effect and is a potential immunomodulator. However, due to the complexity and diversity in the structures and components of GPs, their specific physicochemical properties, and underlying mechanisms remain unclear. In this article, we have summarized the factors influencing the antitumor activity of GPs and their mechanism of action, including the stimulation of the immune system, regulation of the gut microbiota, and direct action on tumor cells.
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Affiliation(s)
- Ruizhi Tao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Keqin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Gangfan Zong
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yawen Xia
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Hongkuan Han
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yang Zhao
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Zhonghong Wei
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
- Corresponding author. Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
| | - Yin Lu
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China
- Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine (TCM) Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China
- Corresponding author. Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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27
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McLean AR, Torres-Morales J, Dewhirst FE, Borisy GG, Welch JLM. Site-tropism of streptococci in the oral microbiome. Mol Oral Microbiol 2022; 37:229-243. [PMID: 36073311 PMCID: PMC9691528 DOI: 10.1111/omi.12387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 08/08/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022]
Abstract
A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.
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Affiliation(s)
- Anthony R. McLean
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
| | | | - Floyd E. Dewhirst
- The Forsyth Institute, Cambridge, MA 02142
- Harvard School of Dental Medicine, Boston, MA 02115
| | | | - Jessica L. Mark Welch
- The Forsyth Institute, Cambridge, MA 02142
- Marine Biological Laboratory, Woods Hole, MA 02543
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28
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Hungatella hathewayi, an Efficient Glycosaminoglycan-Degrading
Firmicutes
from Human Gut and Its Chondroitin ABC Exolyase with High Activity and Broad Substrate Specificity. Appl Environ Microbiol 2022; 88:e0154622. [PMID: 36342199 PMCID: PMC9680638 DOI: 10.1128/aem.01546-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An increased understanding of GAG metabolism by intestinal bacteria is critical in identifying the driving factors for the composition, modulation, and homeostasis of the human gut microbiota. In addition, GAG-depolymerizing polysaccharide lyases are highly desired enzymes for the production of GAG oligosaccharides and as therapeutics.
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29
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Zhang F, Fan D, Huang JL, Zuo T. The gut microbiome: linking dietary fiber to inflammatory diseases. MEDICINE IN MICROECOLOGY 2022. [DOI: 10.1016/j.medmic.2022.100070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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30
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Zhu J, Liu J, Li W, Ru Y, Sun D, Liu C, Li Z, Liu W. Dynamic changes in community structure and degradation performance of a bacterial consortium MMBC-1 during the subculturing revival reveal the potential decomposers of lignocellulose. BIORESOUR BIOPROCESS 2022; 9:110. [PMID: 38647799 PMCID: PMC10991580 DOI: 10.1186/s40643-022-00601-8] [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: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
Bacterial consortium is an important source of lignocellulolytic strains, but it is still a challenge to distinguish the direct decomposers of lignocellulose from other bacteria in such a complex community. This study aims at addressing this issue by focusing on the dynamic changes in community structure and degradation activity of MMBC-1, an established and stable lignocellulolytic bacterial consortium, during its subculturing revival. MMBC-1 was cryopreserved with glycerol as a protective agent and then inoculated for revival. Its enzyme activities for degradation recovered to the maximum level after two rounds of subculturing. Correspondingly, the cellulose and hemicellulose in lignocellulosic carbon source were gradually decomposed during the revival. Meanwhile, the initial dominant bacteria represented by genus Clostridium were replaced by the bacteria belonging to Lachnospira, Enterococcus, Bacillus, Haloimpatiens genera and family Lachnospiraceae. However, only three high-abundance (> 1%) operational taxonomic units (OTUs) (Lachnospira, Enterococcus and Haloimpatiens genera) were suggested to directly engage in lignocellulose degradation according to correlation analysis. By comparison, many low-abundance OTUs, such as the ones belonging to Flavonifractor and Anaerotruncus genera, may play an important role in degradation. These findings showed the dramatic changes in community structure that occurred during the subculturing revival, and paved the way for the discovery of direct decomposers in a stable consortium.
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Affiliation(s)
- Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Weilin Li
- Institutional Center for Shared Technologies and Facilities, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yunrui Ru
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China
| | - Zongyun Li
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life Science, Jiangsu Normal University, No.101, Shanghai Road, Tongshan New District, Xuzhou, 221116, Jiangsu Province, China.
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Hernández-Calderón P, Wiedemann L, Benítez-Páez A. The microbiota composition drives personalized nutrition: Gut microbes as predictive biomarkers for the success of weight loss diets. Front Nutr 2022; 9:1006747. [PMID: 36211501 PMCID: PMC9537590 DOI: 10.3389/fnut.2022.1006747] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/05/2022] [Indexed: 11/26/2022] Open
Abstract
The investigation of the human gut microbiome during recent years has permitted us to understand its relevance for human health at a systemic level, making it possible to establish different functional axes (e.g., the gut-brain, gut-liver, and gut-lung axes), which support the organ-like status conferred to this microecological component of our body. The human gut microbiota is extremely variable but modifiable via diet, a fact that allows targeting of microbes through defined dietary strategies to uncover cost-effective therapies to minimize the burden of non-communicable diseases such as pandemic obesity and overweight and its metabolic comorbidities. Nevertheless, randomly controlled dietary interventions regularly exhibit low to moderate degrees of success in weight control, making their implementation difficult in clinical practice. Here, we review the predictive value of the baseline gut microbiota configurations to anticipate the success of dietary interventions aimed at weight loss, mostly based on caloric restriction regimes and oral fiber supplementation. This emergent research concept fits into precision medicine by considering different diet patterns and adopting the best one, based on the individual microbiota composition, to reach significant adiposity reduction and improve metabolic status. We review the results from this fresh perspective of investigation, taking into account studies released very recently. We also discuss some future outlooks in the field and potential pitfalls to overcome with the aim of gaining knowledge in the field and achieving breakthroughs in personalized nutrition.
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32
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Exploring Bacterial Attributes That Underpin Symbiont Life in the Monogastric Gut. Appl Environ Microbiol 2022; 88:e0112822. [PMID: 36036591 PMCID: PMC9499014 DOI: 10.1128/aem.01128-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The large bowel of monogastric animals, such as that of humans, is home to a microbial community (microbiota) composed of a diversity of mostly bacterial species. Interrelationships between the microbiota as an entity and the host are complex and lifelong and are characteristic of a symbiosis. The relationships may be disrupted in association with disease, resulting in dysbiosis. Modifications to the microbiota to correct dysbiosis require knowledge of the fundamental mechanisms by which symbionts inhabit the gut. This review aims to summarize aspects of niche fitness of bacterial species that inhabit the monogastric gut, especially of humans, and to indicate the research path by which progress can be made in exploring bacterial attributes that underpin symbiont life in the gut.
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Luis AS, Baslé A, Byrne DP, Wright GSA, London JA, Jin C, Karlsson NG, Hansson GC, Eyers PA, Czjzek M, Barbeyron T, Yates EA, Martens EC, Cartmell A. Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota. Nat Chem Biol 2022; 18:841-849. [PMID: 35710619 PMCID: PMC7613211 DOI: 10.1038/s41589-022-01039-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 04/14/2022] [Indexed: 12/31/2022]
Abstract
Sulfated glycans are ubiquitous nutrient sources for microbial communities that have coevolved with eukaryotic hosts. Bacteria metabolize sulfated glycans by deploying carbohydrate sulfatases that remove sulfate esters. Despite the biological importance of sulfatases, the mechanisms underlying their ability to recognize their glycan substrate remain poorly understood. Here, we use structural biology to determine how sulfatases from the human gut microbiota recognize sulfated glycans. We reveal seven new carbohydrate sulfatase structures spanning four S1 sulfatase subfamilies. Structures of S1_16 and S1_46 represent novel structures of these subfamilies. Structures of S1_11 and S1_15 demonstrate how non-conserved regions of the protein drive specificity toward related but distinct glycan targets. Collectively, these data reveal that carbohydrate sulfatases are highly selective for the glycan component of their substrate. These data provide new approaches for probing sulfated glycan metabolism while revealing the roles carbohydrate sulfatases play in host glycan catabolism.
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Affiliation(s)
- Ana S Luis
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden.
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
| | - Dominic P Byrne
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gareth S A Wright
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - James A London
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
- Faculty of Health Sciences, Department of Life Sciences and Health, Pharmacy, Oslo Metropolitan University, Oslo, Norway
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Patrick A Eyers
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Mirjam Czjzek
- Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Tristan Barbeyron
- Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France
| | - Edwin A Yates
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Alan Cartmell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
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Xu A, Zhao Y, Shi Y, Zuo X, Yang Y, Wang Y, Xu P. Effects of oxidation-based tea processing on the characteristics of the derived polysaccharide conjugates and their regulation of intestinal homeostasis in DSS-induced colitis mice. Int J Biol Macromol 2022; 214:402-413. [PMID: 35738342 DOI: 10.1016/j.ijbiomac.2022.06.115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 11/17/2022]
Abstract
Different cultivars and processing technologies involved in producing tea result in the high heterogeneity of derived polysaccharide conjugates, which limits the understanding of their composition and structure, and biological activity. Here, raw tea leaves from the same cultivar were used to produce dried fresh tea leaves, green tea, and black tea, and three polysaccharide conjugates derived from dried fresh tea leaves (FTPS), green tea (GTPS), and black tea (BTPS) were prepared accordingly. Their physiochemical characteristics and bioactivities were investigated. The results showed that the oxidation during tea processing increased the phenolics and proteins while decreasing the GalA in the derived TPS conjugates; meanwhile, it reduced the molecular weight and particle size of BTPS but enhanced their antioxidant activity in vitro. Furthermore, all three TPS conjugates improved intestinal homeostasis by reducing TJ protein loss and inflammation and alleviated DSS-induced colitis symptoms in mice. In addition, the three TPS conjugates showed differential regulation of the intestinal microbiome and altered the produced SCFAs, which contributed to the prevention of colitis. Our findings suggest that TPS conjugates could be applied in colitis prevention in association with the regulation of gut microbiota, and their efficacy could be optimized by employing suitable tea processing technologies.
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Affiliation(s)
- Anan Xu
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Yueling Zhao
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Yuxuan Shi
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Xinxin Zuo
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Yijun Yang
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China
| | - Yuefei Wang
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Ping Xu
- Institute of Tea Science, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China.
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35
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Prebiotics and the Human Gut Microbiota: From Breakdown Mechanisms to the Impact on Metabolic Health. Nutrients 2022; 14:nu14102096. [PMID: 35631237 PMCID: PMC9147914 DOI: 10.3390/nu14102096] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/11/2022] [Accepted: 05/14/2022] [Indexed: 12/13/2022] Open
Abstract
The colon harbours a dynamic and complex community of microorganisms, collectively known as the gut microbiota, which constitutes the densest microbial ecosystem in the human body. These commensal gut microbes play a key role in human health and diseases, revealing the strong potential of fine-tuning the gut microbiota to confer health benefits. In this context, dietary strategies targeting gut microbes to modulate the composition and metabolic function of microbial communities are of increasing interest. One such dietary strategy is the use of prebiotics, which are defined as substrates that are selectively utilised by host microorganisms to confer a health benefit. A better understanding of the metabolic pathways involved in the breakdown of prebiotics is essential to improve these nutritional strategies. In this review, we will present the concept of prebiotics, and focus on the main sources and nature of these components, which are mainly non-digestible polysaccharides. We will review the breakdown mechanisms of complex carbohydrates by the intestinal microbiota and present short-chain fatty acids (SCFAs) as key molecules mediating the dialogue between the intestinal microbiota and the host. Finally, we will review human studies exploring the potential of prebiotics in metabolic diseases, revealing the personalised responses to prebiotic ingestion. In conclusion, we hope that this review will be of interest to identify mechanistic factors for the optimization of prebiotic-based strategies.
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36
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Rawat PS, Seyed Hameed AS, Meng X, Liu W. Utilization of glycosaminoglycans by the human gut microbiota: participating bacteria and their enzymatic machineries. Gut Microbes 2022; 14:2068367. [PMID: 35482895 PMCID: PMC9067506 DOI: 10.1080/19490976.2022.2068367] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Glycosaminoglycans (GAGs) are consistently present in the human colon in free forms and as part of proteoglycans. Their utilization is critical for the colonization and proliferation of gut bacteria and also the health of hosts. Hence, it is essential to determine the GAG-degrading members of the gut bacteria and their enzymatic machinery for GAG depolymerization. In this review, we have summarized the reported GAG utilizers from Bacteroides and presented their polysaccharide utilization loci (PUL) and related enzymatic machineries for the degradation of chondroitin and heparin/heparan sulfate. Although similar comprehensive knowledge of GAG degradation is not available for other gut phyla, we have specified recently isolated GAG degraders from gut Firmicutes and Proteobacteria, and analyzed their genomes for the presence of putative GAG PULs. Deciphering the precise GAG utilization mechanism for various phyla will augment our understanding of their effects on human health.
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Affiliation(s)
- Parkash Singh Rawat
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao266237, P. R. China
| | - Ahkam Saddam Seyed Hameed
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao266237, P. R. China
| | - Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao266237, P. R. China,CONTACT Xiangfeng Meng State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao266237, P. R. China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No.72 Binhai Road, Qingdao266237, P. R. China
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37
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Bloxham B, Lee H, Gore J. Diauxic lags explain unexpected coexistence in multi-resource environments. Mol Syst Biol 2022; 18:e10630. [PMID: 35507445 PMCID: PMC9067609 DOI: 10.15252/msb.202110630] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/09/2022] Open
Abstract
How the coexistence of species is affected by the presence of multiple resources is a major question in microbial ecology. We experimentally demonstrate that differences in diauxic lags, which occur as species deplete their own environments and adapt their metabolisms, allow slow-growing microbes to stably coexist with faster-growing species in multi-resource environments despite being excluded in single-resource environments. In our focal example, an Acinetobacter species (Aci2) competitively excludes Pseudomonas aurantiaca (Pa) on alanine and on glutamate. However, they coexist on the combination of both resources. Experiments reveal that Aci2 grows faster but Pa has shorter diauxic lags. We establish a tradeoff between Aci2's fast growth and Pa's short lags as their mechanism for coexistence. We model this tradeoff to accurately predict how environmental changes affect community composition. We extend our work by surveying a large set of competitions and observe coexistence nearly four times as frequently when the slow-grower is the fast-switcher. Our work illustrates a simple mechanism, based entirely on supplied-resource growth dynamics, for the emergence of multi-resource coexistence.
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Affiliation(s)
- Blox Bloxham
- Physics of Living SystemsDepartment of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Hyunseok Lee
- Physics of Living SystemsDepartment of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
| | - Jeff Gore
- Physics of Living SystemsDepartment of PhysicsMassachusetts Institute of TechnologyCambridgeMAUSA
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38
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Gu J, Mao B, Cui S, Tang X, Liu Z, Zhao J, Zhang H. Bifidobacteria exhibited stronger ability to utilize fructooligosaccharides, compared with other bacteria in the mouse intestine. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:2413-2423. [PMID: 34628644 DOI: 10.1002/jsfa.11580] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/25/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Fructooligosaccharides (FOS) have been identified as important prebiotics. Previous studies have found that they can significantly promote the proliferation of Bifidobacterium pseudolongum in the mouse intestine. However, it is still unclear which other bacteria in the mouse intestine can utilize FOS, and the differences in the ability to utilize FOS. In this study, the bacteria capable of utilizing FOS were isolated from mice feces and their ability to utilize FOS was compared. Draft genome sequencing was also applied to explain the differences in FOS utilization at the gene levels. RESULTS A total of 15 species were isolated from mouse feces and 13 species were able to utilize fructofuranosylnystose (GF2). Eleven species could utilize nistose (GF3), but not Enterococcus hirae and Lactobacillus reuteri. In contrast, 1-kestose (GF4) was hardly utilized. The enzyme activity determination and draft genome sequencing-based analyses revealed that all isolated species used the phosphotransferase system or permease system to transport FOS into the cells before hydrolysis by β-fructofuranosidase. Although β-fructofuranosidase exists in all strains, there are big differences in the corresponding coding genes between bifidobacteria and non-bifidobacteria. CONCLUSION Compared with the other isolates, Bifidobacterium species exhibited higher enzyme activity and shorter generation time, leading to a stronger ability to utilize FOS. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Jiayu Gu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Shumao Cui
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Xin Tang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Zhenmin Liu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd, Shanghai, P. R. China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- School of Food Science and Technology, Jiangnan University, Wuxi, P. R. China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, P. R. China
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39
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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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40
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Feng J, Qian Y, Zhou Z, Ertmer S, Vivas EI, Lan F, Hamilton JJ, Rey FE, Anantharaman K, Venturelli OS. Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions. Cell Host Microbe 2022; 30:200-215.e12. [PMID: 34995484 PMCID: PMC9060796 DOI: 10.1016/j.chom.2021.12.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/22/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023]
Abstract
Polysaccharide utilization loci (PULs) are co-regulated bacterial genes that sense nutrients and enable glycan digestion. Human gut microbiome members, notably Bacteroides, contain numerous PULs that enable glycan utilization and shape ecological dynamics. To investigate the role of PULs on fitness and inter-species interactions, we develop a CRISPR-based genome editing tool to study 23 PULs in Bacteroides uniformis (BU). BU PULs show distinct glycan-degrading functions and transcriptional coordination that enables the population to adapt upon loss of other PULs. Exploiting a BU mutant barcoding strategy, we demonstrate that in vitro fitness and BU colonization in the murine gut are enhanced by deletion of specific PULs and modulated by glycan availability. PULs mediate glycan-dependent interactions with butyrate producers that depend on the degradation mechanism and glycan utilization ability of the butyrate producer. Thus, PULs determine community dynamics and butyrate production and provide a selective advantage or disadvantage depending on the nutritional landscape.
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Affiliation(s)
- Jun Feng
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zhichao Zhou
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sarah Ertmer
- Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Eugenio I. Vivas
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA,Gnotobiotic Animal Core Facility, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Freeman Lan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J. Hamilton
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Federico E. Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Karthik Anantharaman
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ophelia S. Venturelli
- The Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA,Department of Chemical & Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA,Lead contact,Correspondence:
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41
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Li C, Hu Y. New definition of resistant starch types from the gut microbiota perspectives - a review. Crit Rev Food Sci Nutr 2022; 63:6412-6422. [PMID: 35075962 DOI: 10.1080/10408398.2022.2031101] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Current definition of resistant starch (RS) types is largely based on their interactions with digestive enzymes from human upper gastrointestinal tract. However, this is frequently inadequate to reflect their effects on the gut microbiota, which is an important mechanism for RS to fulfill its function to improve human health. Distinct shifts of gut microbiota compositions and alterations of fermented metabolites could be resulted by the consumption of RS from the same type. This review summarized these defects from the current definitions of RS types, while more importantly proposed pioneering concepts for new definitions of RS types from the gut microbiota perspectives. New RS types considered the aspects of RS fermentation rate, fermentation end products, specificity toward gut microbiota and shifts of gut microbiota caused by the consumption of RS. These definitions were depending on the known outcomes from RS-gut microbiota interactions. The application of new RS types in understanding the complex RS-gut microbiota interactions and promoting human health should be focused in the future.
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Affiliation(s)
- Cheng Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yiming Hu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
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Foster-Nyarko E, Pallen MJ. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6522174. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's ‘rock star’, driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance—including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
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Affiliation(s)
- Ebenezer Foster-Nyarko
- Corresponding author: Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom. E-mail:
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
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43
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Zimmermann C, Wagner AE. Impact of Food-Derived Bioactive Compounds on Intestinal Immunity. Biomolecules 2021; 11:biom11121901. [PMID: 34944544 PMCID: PMC8699755 DOI: 10.3390/biom11121901] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
The gastrointestinal system is responsible for the digestion and the absorption of nutrients. At the same time, it is essentially involved in the maintenance of immune homeostasis. The strongest antigen contact in an organism takes place in the digestive system showing the importance of a host to develop mechanisms allowing to discriminate between harmful and harmless antigens. An efficient intestinal barrier and the presence of a large and complex part of the immune system in the gut support the host to implement this task. The continuous ingestion of harmless antigens via the diet requires an efficient immune response to reliably identify them as safe. However, in some cases the immune system accidentally identifies harmless antigens as dangerous leading to various diseases such as celiac disease, inflammatory bowel diseases and allergies. It has been shown that the intestinal immune function can be affected by bioactive compounds derived from the diet. The present review provides an overview on the mucosal immune reactions in the gut and how bioactive food ingredients including secondary plant metabolites and probiotics mediate its health promoting effects with regard to the intestinal immune homeostasis.
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Complementary resource preferences spontaneously emerge in diauxic microbial communities. Nat Commun 2021; 12:6661. [PMID: 34795267 PMCID: PMC8602314 DOI: 10.1038/s41467-021-27023-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 10/25/2021] [Indexed: 01/04/2023] Open
Abstract
Many microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that unlike co-utilizing communities, diauxic community assembly repeatably and spontaneously leads to communities with complementary resource preferences, namely communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a diauxic species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes.
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45
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Hu Y, Li C, Hou Y. Possible regulation of liver glycogen structure through the gut-liver axis by resistant starch: a review. Food Funct 2021; 12:11154-11164. [PMID: 34694313 DOI: 10.1039/d1fo02416g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Liver glycogen α particles in diabetic patients are fragile relative to those in healthy individuals, and restoring these fragile glycogen particles to a normal state shows potential to contribute to the remission of diabetes. Resistant starch (RS) is beneficial for diabetes management through its interactions with the gut microbiota. However, its effects on glycogen fragility are not fully understood. This review aims to summarize the recent understanding of the interactions between RS and the human gut microbiota and the possible connections to liver glycogen biosynthesis to elucidate its role in the development of glycogen fragility. RS might regulate glycogen fragility in diabetes by modulating the postprandial glycemic response and glycogen biosynthesis pathways. Before RS can be applied to repair fragile glycogen, more work should be done to better understand in vivo RS structures and identify the factor binding glycogen β particles together. This review contains important information on the connections between glycogen fragility and RS-gut microbiota interactions, which could help to better understand the health benefits of RS consumption.
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Affiliation(s)
- Yiming Hu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200031, China.
| | - Cheng Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China.
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200031, China.
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46
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Abstract
The aim of this review is to provide an overview of the complex interactions between dietary fibre and the resident microbial community in the human gut. The microbiota influences both health maintenance and disease development. In the large intestine, the microbiota plays a crucial role in the degradation of dietary carbohydrates that remain undigested in the upper gut (non-digestible carbohydrates or fibre). Dietary fibre contains a variety of different types of carbohydrates, and its breakdown is facilitated by many different microbial enzymes. Some microbes, termed generalists, are able to degrade a range of different carbohydrates, whereas others are more specialised. Furthermore, the physicochemical characteristics of dietary fibre, such as whether it enters the gut in soluble or insoluble form, also likely influence which microbes can degrade it. A complex nutritional network therefore exists comprising primary degraders able to attack complex fibre and cross feeders that benefit from fibre breakdown intermediates or fermentation products. This leads predominately to the generation of the short-chain fatty acids (SCFA) acetate, propionate and butyrate, which exert various effects on host physiology, including the supply of energy, influencing glucose and lipid metabolism and anti-carcinogenic and anti-inflammatory actions. In order to effectively modulate the gut microbiota through diet, there is a need to better understand the complex competitive and cooperative interactions between gut microbes in dietary fibre breakdown, as well as how gut environmental factors and the physicochemical state of fibre originating from different types of diets influence microbial metabolism and ecology in the gut.
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47
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Pudlo NA, Martens EC. Small RNAs Go Global in Human Gut Bacteroides. J Bacteriol 2021; 203:e0038321. [PMID: 34370557 PMCID: PMC8508101 DOI: 10.1128/jb.00383-21] [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] [Indexed: 11/20/2022] Open
Abstract
The last two decades have seen numerous studies connecting physiological behaviors in Bacteroides-including polysaccharide degradation and capsule production-with elements of global regulation, but a complete model is still elusive. A new study by Adams et al. in this issue of the Journal of Bacteriology reveals another layer of regulation by describing a novel family of RNA-binding proteins in Bacteroides thetaiotaomicron that modify expression of genes involved in carbohydrate utilization and capsule expression, among others (A. N. D. Adams, M. S. Azam, Z. A. Costliow, X. Ma, et al., J Bacteriol 203:e00217-21, 2021, https://doi.org/10.1128/JB.00217-21).
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Affiliation(s)
- Nicholas A. Pudlo
- 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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48
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Sichert A, Cordero OX. Polysaccharide-Bacteria Interactions From the Lens of Evolutionary Ecology. Front Microbiol 2021; 12:705082. [PMID: 34690949 PMCID: PMC8531407 DOI: 10.3389/fmicb.2021.705082] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
Microbes have the unique ability to break down the complex polysaccharides that make up the bulk of organic matter, initiating a cascade of events that leads to their recycling. Traditionally, the rate of organic matter degradation is perceived to be limited by the chemical and physical structure of polymers. Recent advances in microbial ecology, however, suggest that polysaccharide persistence can result from non-linear growth dynamics created by the coexistence of alternate degradation strategies, metabolic roles as well as by ecological interactions between microbes. This complex "landscape" of degradation strategies and interspecific interactions present in natural microbial communities appears to be far from evolutionarily stable, as frequent gene gain and loss reshape enzymatic repertoires and metabolic roles. In this perspective, we discuss six challenges at the heart of this problem, ranging from the evolution of genetic repertoires, phenotypic heterogeneity in clonal populations, the development of a trait-based ecology, and the impact of metabolic interactions and microbial cooperation on degradation rates. We aim to reframe some of the key questions in the study of polysaccharide-bacteria interactions in the context of eco-evolutionary dynamics, highlighting possible research directions that, if pursued, would advance our understanding of polysaccharide degraders at the interface between biochemistry, ecology and evolution.
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49
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McKee LS, La Rosa SL, Westereng B, Eijsink VG, Pope PB, Larsbrink J. Polysaccharide degradation by the Bacteroidetes: mechanisms and nomenclature. ENVIRONMENTAL MICROBIOLOGY REPORTS 2021; 13:559-581. [PMID: 34036727 DOI: 10.1111/1758-2229.12980] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 05/22/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
The Bacteroidetes phylum is renowned for its ability to degrade a wide range of complex carbohydrates, a trait that has enabled its dominance in many diverse environments. The best studied species inhabit the human gut microbiome and use polysaccharide utilization loci (PULs), discrete genetic structures that encode proteins involved in the sensing, binding, deconstruction, and import of target glycans. In many environmental species, polysaccharide degradation is tightly coupled to the phylum-exclusive type IX secretion system (T9SS), which is used for the secretion of certain enzymes and is linked to gliding motility. In addition, within specific species these two adaptive systems (PULs and T9SS) are intertwined, with PUL-encoded enzymes being secreted by the T9SS. Here, we discuss the most noteworthy PUL and non-PUL mechanisms that confer specific and rapid polysaccharide degradation capabilities to the Bacteroidetes in a range of environments. We also acknowledge that the literature showcasing examples of PULs is rapidly expanding and developing a set of assumptions that can be hard to track back to original findings. Therefore, we present a simple universal description of conserved PUL functions and how they are determined, while proposing a common nomenclature describing PULs and their components, to simplify discussion and understanding of PUL systems.
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Affiliation(s)
- Lauren S McKee
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
| | | | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Vincent G Eijsink
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Phillip B Pope
- Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Johan Larsbrink
- Wallenberg Wood Science Center, Stockholm, 100 44, Sweden
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, 412 96, Sweden
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50
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Li C, Hu Y. Align resistant starch structures from plant-based foods with human gut microbiome for personalized health promotion. Crit Rev Food Sci Nutr 2021; 63:2509-2520. [PMID: 34515592 DOI: 10.1080/10408398.2021.1976722] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Resistant starch (RS) is beneficial for human health through its interactions with gut microbiota. However, the alignment between RS structures with gut microbiota profile and consequentially health benefits remain elusive. This review summarizes current understanding of RS complex structures and their interactions with the gut microbiota, aiming to highlight the possibility of manipulating RS structures for a targeted and predictable gut microbiota shift for human health in a personalized way. Current definition of RS types is strongly associated with starch digestion behaviors in small intestine, which does not precisely reflect their interactions with human gut microbiota. Distinct alterations of gut microbiota could be associated with the same RS type. The principles to describe the specificity of different RS structural characteristics in terms of aligning with human gut microbiota shift was proposed in this review, which could result in new definitions of RS types from the microbial perspectives. To consider the highly variable personal features, a machine-learning algorithm to integrate different personalized factors and better understand the complex interaction between RS and gut microbiota and its effects on individual health was explained. This review contains important information to bring interactions between RS and gut microbiota to translational practice.
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Affiliation(s)
- Cheng Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yiming Hu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
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