51
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Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting. Nat Commun 2023; 14:662. [PMID: 36750571 PMCID: PMC9905522 DOI: 10.1038/s41467-023-36365-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/26/2023] [Indexed: 02/09/2023] Open
Abstract
The composition and metabolism of the human gut microbiota are strongly influenced by dietary complex glycans, which cause downstream effects on the physiology and health of hosts. Despite recent advances in our understanding of glycan metabolism by human gut bacteria, we still need methods to link glycans to their consuming bacteria. Here, we use a functional assay to identify and isolate gut bacteria from healthy human volunteers that take up different glycans. The method combines metabolic labeling using fluorescent oligosaccharides with fluorescence-activated cell sorting (FACS), followed by amplicon sequencing or culturomics. Our results demonstrate metabolic labeling in various taxa, such as Prevotella copri, Collinsella aerofaciens and Blautia wexlerae. In vitro validation confirms the ability of most, but not all, labeled species to consume the glycan of interest for growth. In parallel, we show that glycan consumers spanning three major phyla can be isolated from cultures of sorted labeled cells. By linking bacteria to the glycans they consume, this approach increases our basic understanding of glycan metabolism by gut bacteria. Going forward, it could be used to provide insight into the mechanism of prebiotic approaches, where glycans are used to manipulate the gut microbiota composition.
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Hayase E, Hayase T, Mukherjee A, Stinson SC, Jamal MA, Ortega MR, Sanchez CA, Ahmed SS, Karmouch JL, Chang CC, Flores II, McDaniel LK, Brown AN, El-Himri RK, Chapa VA, Tan L, Tran BQ, Pham D, Halsey TM, Jin Y, Tsai WB, Prasad R, Glover IK, Ajami NJ, Wargo JA, Shelburne S, Okhuysen PC, Liu C, Fowler SW, Conner ME, Peterson CB, Rondon G, Molldrem JJ, Champlin RE, Shpall EJ, Lorenzi PL, Mehta RS, Martens EC, Alousi AM, Jenq RR. Bacteroides ovatus alleviates dysbiotic microbiota-induced intestinal graft-versus-host disease. RESEARCH SQUARE 2023:rs.3.rs-2460097. [PMID: 36778495 PMCID: PMC9915792 DOI: 10.21203/rs.3.rs-2460097/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Acute gastrointestinal intestinal GVHD (aGI-GVHD) is a serious complication of allogeneic hematopoietic stem cell transplantation, and the intestinal microbiota is known to impact on its severity. However, an association between treatment response of aGI-GVHD and the intestinal microbiota has not been well-studied. In a cohort of patients with aGI-GVHD (n=37), we found that non-response to standard therapy with corticosteroids was associated with prior treatment with carbapenem antibiotics and loss of Bacteroides ovatus from the microbiome. In a mouse model of carbapenem-aggravated GVHD, introducing Bacteroides ovatus reduced severity of GVHD and improved survival. Bacteroides ovatus reduced degradation of colonic mucus by another intestinal commensal, Bacteroides thetaiotaomicron, via its ability to metabolize dietary polysaccharides into monosaccharides, which then inhibit mucus degradation by Bacteroides thetaiotaomicron and reduce GVHD-related mortality.
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Affiliation(s)
- Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Akash Mukherjee
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Stuart C. Stinson
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Mohamed A. Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Miriam R. Ortega
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Christopher A. Sanchez
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Saira S. Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Jennifer L. Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Ivonne I. Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Lauren K. McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Alexandria N. Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Rawan K. El-Himri
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Valerie A. Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Lin Tan
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Bao Q. Tran
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Dung Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Taylor M. Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Israel K. Glover
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Nadim J. Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Jennifer A. Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
| | - Samuel Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Pablo C. Okhuysen
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Stephanie W. Fowler
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Comparative Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret E. Conner
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christine B. Peterson
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jeffrey J. Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Richard E. Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Philip L. Lorenzi
- Metabolomics Core Facility, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Rohtesh S. Mehta
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Eric C. Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Amin M. Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Robert R. Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
- CPRIT Scholar in Cancer Research, Houston, Texas, USA
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53
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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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54
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Ostrem Loss E, Thompson J, Cheung PLK, Qian Y, Venturelli OS. Carbohydrate complexity limits microbial growth and reduces the sensitivity of human gut communities to perturbations. Nat Ecol Evol 2023; 7:127-142. [PMID: 36604549 DOI: 10.1038/s41559-022-01930-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 10/10/2022] [Indexed: 01/07/2023]
Abstract
Dietary fibre impacts the growth dynamics of human gut microbiota, yet we lack a detailed and quantitative understanding of how these nutrients shape microbial interaction networks and responses to perturbations. By building human gut communities coupled with computational modelling, we dissect the effects of fibres that vary in chemical complexity and each of their constituent sugars on community assembly and response to perturbations. We demonstrate that the degree of chemical complexity across different fibres limits microbial growth and the number of species that can utilize these nutrients. The prevalence of negative interspecies interactions is reduced in the presence of fibres compared with their constituent sugars. Carbohydrate chemical complexity enhances the reproducibility of community assembly and resistance of the community to invasion. We demonstrate that maximizing or minimizing carbohydrate competition between resident and invader species enhances resistance to invasion. In sum, the quantitative effects of carbohydrate chemical complexity on microbial interaction networks could be exploited to inform dietary and bacterial interventions to modulate community resistance to perturbations.
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Affiliation(s)
- Erin Ostrem Loss
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Jaron Thompson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Yili Qian
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ophelia S Venturelli
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA. .,Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, USA.
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55
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Pearce VH, Groisman EA, Townsend GE. Dietary sugars silence the master regulator of carbohydrate utilization in human gut Bacteroides species. Gut Microbes 2023; 15:2221484. [PMID: 37358144 PMCID: PMC10294740 DOI: 10.1080/19490976.2023.2221484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/08/2023] [Indexed: 06/27/2023] Open
Abstract
The mammalian gut microbiota is a critical human health determinant with therapeutic potential for remediation of many diseases. The host diet is a key factor governing the gut microbiota composition by altering nutrient availability and supporting the expansion of distinct microbial populations. Diets rich in simple sugars modify the abundance of microbial subsets, enriching for microbiotas that elicit pathogenic outcomes. We previously demonstrated that diets rich in fructose and glucose can reduce the fitness and abundance of a human gut symbiont, Bacteroides thetaiotaomicron, by silencing the production of a critical intestinal colonization protein, called Roc, via its mRNA leader through an unknown mechanism. We have now determined that dietary sugars silence Roc by reducing the activity of BT4338, a master regulator of carbohydrate utilization. Here, we demonstrate that BT4338 is required for Roc synthesis, and that BT4338 activity is silenced by glucose or fructose. We show that the consequences of glucose and fructose on orthologous transcription factors are conserved across human intestinal Bacteroides species. This work identifies a molecular pathway by which a common dietary additive alters microbial gene expression in the gut that could be harnessed to modulate targeted microbial populations for future therapeutic interventions.
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Affiliation(s)
- Victoria H. Pearce
- Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
- Penn State Microbiome Center, Pennsylvania State University, State College, PA, USA
- Center for Molecular Carcinogenesis and Toxicology, Pennsylvania State University, State College, PA, USA
| | - Eduardo A. Groisman
- Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Microbial Sciences Institute, Yale University, New Haven, CT, USA
| | - Guy E. Townsend
- Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
- Penn State Microbiome Center, Pennsylvania State University, State College, PA, USA
- Center for Molecular Carcinogenesis and Toxicology, Pennsylvania State University, State College, PA, USA
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56
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Betancur-Murillo CL, Aguilar-Marín SB, Jovel J. Prevotella: A Key Player in Ruminal Metabolism. Microorganisms 2022; 11:microorganisms11010001. [PMID: 36677293 PMCID: PMC9866204 DOI: 10.3390/microorganisms11010001] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Ruminants are foregut fermenters that have the remarkable ability of converting plant polymers that are indigestible to humans into assimilable comestibles like meat and milk, which are cornerstones of human nutrition. Ruminants establish a symbiotic relationship with their microbiome, and the latter is the workhorse of carbohydrate fermentation. On the other hand, during carbohydrate fermentation, synthesis of propionate sequesters H, thus reducing its availability for the ultimate production of methane (CH4) by methanogenic archaea. Biochemically, methane is the simplest alkane and represents a downturn in energetic efficiency in ruminants; environmentally, it constitutes a potent greenhouse gas that negatively affects climate change. Prevotella is a very versatile microbe capable of processing a wide range of proteins and polysaccharides, and one of its fermentation products is propionate, a trait that appears conspicuous in P. ruminicola strain 23. Since propionate, but not acetate or butyrate, constitutes an H sink, propionate-producing microbes have the potential to reduce methane production. Accordingly, numerous studies suggest that members of the genus Prevotella have the ability to divert the hydrogen flow in glycolysis away from methanogenesis and in favor of propionic acid production. Intended for a broad audience in microbiology, our review summarizes the biochemistry of carbohydrate fermentation and subsequently discusses the evidence supporting the essential role of Prevotella in lignocellulose processing and its association with reduced methane emissions. We hope this article will serve as an introduction to novice Prevotella researchers and as an update to others more conversant with the topic.
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Affiliation(s)
- Claudia Lorena Betancur-Murillo
- Escuela de Ciencias Básicas, Tecnología e Ingeniería, Universidad Nacional Abierta y a Distancia, UNAD, Bogotá 111511, Colombia
| | | | - Juan Jovel
- Faculty of Veterinary Medicine, University of Calgary, 3280 Hospital Dr NW, Calgary, AB T2N 4Z6, Canada
- Correspondence:
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57
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Cohen Y, Borenstein E. The microbiome's fiber degradation profile and its relationship with the host diet. BMC Biol 2022; 20:266. [PMID: 36464700 PMCID: PMC9721016 DOI: 10.1186/s12915-022-01461-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/08/2022] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The relationship between the gut microbiome and diet has been the focus of numerous recent studies. Such studies aim to characterize the impact of diet on the composition of the microbiome, as well as the microbiome's ability to utilize various compounds in the diet and produce metabolites that may be beneficial for the host. Consumption of dietary fibers (DFs)-polysaccharides that cannot be broken down by the host's endogenous enzymes and are degraded primarily by members of the microbiome-is known to have a profound effect on the microbiome. Yet, a comprehensive characterization of microbiome compositional and functional shifts in response to the consumption of specific DFs is still lacking. RESULTS Here, we introduce a computational framework, coupling metagenomic sequencing with careful annotation of polysaccharide degrading enzymes and DF structures, for inferring the metabolic ability of a given microbiome sample to utilize a broad catalog of DFs. We demonstrate that the inferred fiber degradation profile (IFDP) generated by our framework accurately reflects the dietary habits of various hosts across four independent datasets. We further demonstrate that IFDPs are more tightly linked to the host diet than commonly used taxonomic and functional microbiome-based profiles. Finally, applying our framework to a set of ~700 metagenomes that represents large human population cohorts from 9 different countries, we highlight intriguing global patterns linking DF consumption habits with microbiome capacities. CONCLUSIONS Combined, our findings serve as a proof-of-concept for the use of DF-specific analysis for providing important complementary information for better understanding the relationship between dietary habits and the gut microbiome.
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Affiliation(s)
- Yotam Cohen
- grid.12136.370000 0004 1937 0546The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Elhanan Borenstein
- grid.12136.370000 0004 1937 0546The Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel ,grid.12136.370000 0004 1937 0546Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel ,grid.209665.e0000 0001 1941 1940Santa Fe Institute, Santa Fe, NM USA
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58
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Dodd D, Cann I. Tutorial: Microbiome studies in drug metabolism. Clin Transl Sci 2022; 15:2812-2837. [PMID: 36099474 PMCID: PMC9747132 DOI: 10.1111/cts.13416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 07/20/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
The human gastrointestinal tract is home to a dense population of microorganisms whose metabolism impacts human health and physiology. The gut microbiome encodes millions of genes, the products of which endow our bodies with unique biochemical activities. In the context of drug metabolism, microbial biochemistry in the gut influences humans in two major ways: (1) by producing small molecules that modulate expression and activity of human phase I and II pathways; and (2) by directly modifying drugs administered to humans to yield active, inactive, or toxic metabolites. Although the capacity of the microbiome to modulate drug metabolism has long been known, recent studies have explored these interactions on a much broader scale and have revealed an unprecedented scope of microbial drug metabolism. The implication of this work is that we might be able to predict the capacity of an individual's microbiome to metabolize drugs and use this information to avoid toxicity and inform proper dosing. Here, we provide a tutorial of how to study the microbiome in the context of drug metabolism, focusing on in vitro, rodent, and human studies. We then highlight some limitations and opportunities for the field.
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Affiliation(s)
- Dylan Dodd
- Department of PathologyStanford University School of MedicineStanfordCaliforniaUSA,Department of Microbiology and ImmunologyStanford University School of MedicineStanfordCaliforniaUSA
| | - Isaac Cann
- Department of Animal ScienceUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Carl R. Woese Institute for Genomic Biology (Microbiome Metabolic Engineering Theme)University of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Division of Nutritional SciencesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Center for East Asian & Pacific StudiesUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA,Department of MicrobiologyUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
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59
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Zheng J, Hu B, Zhang X, Ge Q, Yan Y, Akresi J, Piyush V, Huang L, Yin Y. dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes. Nucleic Acids Res 2022; 51:D557-D563. [PMID: 36399503 PMCID: PMC9825555 DOI: 10.1093/nar/gkac1068] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.
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Affiliation(s)
| | | | | | - Qiwei Ge
- School of Computing, University of Nebraska, Lincoln, NE 68588, USA
| | - Yuchen Yan
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Jerry Akresi
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68588, USA
| | - Ved Piyush
- Department of Statistics, University of Nebraska, Lincoln, NE 68588, USA
| | - Le Huang
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, NC, USA
| | - Yanbin Yin
- To whom correspondence should be addressed. Tel: +1 402 472 4303; Fax: +1 402 472 2831;
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60
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Letourneau J, Holmes ZC, Dallow EP, Durand HK, Jiang S, Carrion VM, Gupta SK, Mincey AC, Muehlbauer MJ, Bain JR, David LA. Ecological memory of prior nutrient exposure in the human gut microbiome. THE ISME JOURNAL 2022; 16:2479-2490. [PMID: 35871250 PMCID: PMC9563064 DOI: 10.1038/s41396-022-01292-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 04/20/2023]
Abstract
Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, whether microbial communities alter their response to repeated stimulus remains incompletely understood. Using the human gut microbiome as a model, we show that bacterial communities retain an "ecological memory" of past carbohydrate exposures. Memory of the prebiotic inulin was encoded within a day of supplementation among a cohort of human study participants. Using in vitro gut microbial models, we demonstrated that the strength of ecological memory scales with nutrient dose and persists for days. We found evidence that memory is seeded by transcriptional changes among primary degraders of inulin within hours of nutrient exposure, and that subsequent changes in the activity and abundance of these taxa are sufficient to enhance overall community nutrient metabolism. We also observed that ecological memory of one carbohydrate species impacts microbiome response to other carbohydrates, and that an individual's habitual exposure to dietary fiber was associated with their gut microbiome's efficiency at digesting inulin. Together, these findings suggest that the human gut microbiome's metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. The dynamics of this ecological memory also highlight the potential for intra-individual microbiome variation to affect the design and interpretation of interventions involving the gut microbiome.
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Affiliation(s)
- Jeffrey Letourneau
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Eric P Dallow
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Heather K Durand
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Sharon Jiang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Verónica M Carrion
- Duke Office of Clinical Research, Duke University School of Medicine, Durham, NC, USA
| | - Savita K Gupta
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Adam C Mincey
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - Michael J Muehlbauer
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
| | - James R Bain
- Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA
- Department of Medicine (Endocrinology), Duke University School of Medicine, Durham, NC, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA.
- Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
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61
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Nakajima M. β-1,2-Glucans and associated enzymes. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01205-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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62
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Hayase E, Hayase T, Jamal MA, Miyama T, Chang CC, Ortega MR, Ahmed SS, Karmouch JL, Sanchez CA, Brown AN, El-Himri RK, Flores II, McDaniel LK, Pham D, Halsey T, Frenk AC, Chapa VA, Heckel BE, Jin Y, Tsai WB, Prasad R, Tan L, Veillon L, Ajami NJ, Wargo JA, Galloway-Peña J, Shelburne S, Chemaly RF, Davey L, Glowacki RWP, Liu C, Rondon G, Alousi AM, Molldrem JJ, Champlin RE, Shpall EJ, Valdivia RH, Martens EC, Lorenzi PL, Jenq RR. Mucus-degrading Bacteroides link carbapenems to aggravated graft-versus-host disease. Cell 2022; 185:3705-3719.e14. [PMID: 36179667 PMCID: PMC9542352 DOI: 10.1016/j.cell.2022.09.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 06/15/2022] [Accepted: 08/31/2022] [Indexed: 01/26/2023]
Abstract
The intestinal microbiota is an important modulator of graft-versus-host disease (GVHD), which often complicates allogeneic hematopoietic stem cell transplantation (allo-HSCT). Broad-spectrum antibiotics such as carbapenems increase the risk for intestinal GVHD, but mechanisms are not well understood. In this study, we found that treatment with meropenem, a commonly used carbapenem, aggravates colonic GVHD in mice via the expansion of Bacteroides thetaiotaomicron (BT). BT has a broad ability to degrade dietary polysaccharides and host mucin glycans. BT in meropenem-treated allogeneic mice demonstrated upregulated expression of enzymes involved in the degradation of mucin glycans. These mice also had thinning of the colonic mucus layer and decreased levels of xylose in colonic luminal contents. Interestingly, oral xylose supplementation significantly prevented thinning of the colonic mucus layer in meropenem-treated mice. Specific nutritional supplementation strategies, including xylose supplementation, may combat antibiotic-mediated microbiome injury to reduce the risk for intestinal GVHD in allo-HSCT patients.
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Affiliation(s)
- Eiko Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Tomo Hayase
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Mohamed A Jamal
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Takahiko Miyama
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Chia-Chi Chang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Miriam R Ortega
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Saira S Ahmed
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jennifer L Karmouch
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Christopher A Sanchez
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Alexandria N Brown
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Rawan K El-Himri
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Ivonne I Flores
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Lauren K McDaniel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Dung Pham
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Taylor Halsey
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Annette C Frenk
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Valerie A Chapa
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Brooke E Heckel
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Yimei Jin
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Wen-Bin Tsai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Rishika Prasad
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Lin Tan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA; Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Lucas Veillon
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA; Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Nadim J Ajami
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jennifer A Wargo
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Jessica Galloway-Peña
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Veterinary Pathobiology, Interdisciplinary Program in Genetics, Texas A&M University, College Station, TX 77843, USA
| | - Samuel Shelburne
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Roy F Chemaly
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lauren Davey
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Robert W P Glowacki
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Chen Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriela Rondon
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Amin M Alousi
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeffrey J Molldrem
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Richard E Champlin
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA
| | - Eric C Martens
- Department of Microbiology & Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Philip L Lorenzi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77230, USA; Metabolomics Core Facility, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Robert R Jenq
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; CPRIT Scholar in Cancer Research, Houston, TX, USA.
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63
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A Novel Carrageenan Metabolic Pathway in Flavobacterium algicola. Appl Environ Microbiol 2022; 88:e0110022. [PMID: 36036580 PMCID: PMC9499021 DOI: 10.1128/aem.01100-22] [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: 11/20/2022] Open
Abstract
Carbohydrate-active enzymes are important components of the polysaccharide metabolism system in marine bacteria. Carrageenase is indispensable for forming carrageenan catalytic pathways. Here, two GH16_13 carrageenases showed likely hydrolysis activities toward different types of carrageenans (e.g., κ-, hybrid β/κ, hybrid α/ι, and hybrid λ), which indicates that a novel pathway is present in the marine bacterium Flavobacterium algicola to use κ-carrageenan (KC), ι-carrageenan (IC), and λ-carrageenan (LC). A comparative study described the different features with another reported pathway based on the specific carrageenans (κ, ι, and λ) and expanded the carrageenan metabolic versatility in F. algicola. A further comparative genomic analysis of carrageenan-degrading bacteria indicated different distributions of carrageenan metabolism-related genes in marine bacteria. The crucial core genes encoding the GH127 α-3,6-anhydro-d-galactosidase (ADAG) and 3,6-anhydro-d-galactose (d-AHG)-utilized cluster have been conserved during evolution. This analysis further revealed the horizontal gene transfer (HGT) phenomenon of the carrageenan polysaccharide utilization loci (CarPUL) from Bacteroidetes to other bacterial phyla, as well as the versatility of carrageenan catalytic activities in marine bacteria through different metabolic pathways. IMPORTANCE Based on the premise that the specific carrageenan-based pathway involved in carrageenan use by Flavobacterium algicola has been identified, another pathway was further analyzed, and it involved two GH16_13 carrageenases. Among all the characterized carrageenases, the members of GH16_13 accounted for only a small portion. Here, the functional analysis of two GH16_13 carrageenases suggested their hydrolysis effects on different types of carrageenans (e.g., κ, hybrid β/κ, hybrid α/ι-, and hybrid λ-), which led to the identification of another pathway. Further exploration enabled us to elucidate the novel pathway that metabolizes KC and IC in F. algicola successfully. The coexistence of these two pathways may provide improved survivability by F. algicola in the marine environment.
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64
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Structural and Biochemical Characterization of a Nonbinding SusD-Like Protein Involved in Xylooligosaccharide Utilization by an Uncultured Human Gut Bacteroides Strain. mSphere 2022; 7:e0024422. [PMID: 36043703 PMCID: PMC9599597 DOI: 10.1128/msphere.00244-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the human gut microbiota, Bacteroidetes break down dietary and endogenous glycosides through highly specific polysaccharide utilization loci (PULs). PULs encode a variety of sensor regulators, binding proteins, transporters, and carbohydrate-active enzymes (CAZymes). Surface glycan-binding proteins (SGBPs) are essential for the efficient capture of the glycosides present on the cell surface, providing Bacteroidetes with a competitive advantage in colonizing their habitats. Here, we present the functional and structural characterization of a SusD-like protein encoded by a xylooligosaccharide (XOS) PUL from an uncultured human gut Bacteroides strain. This locus is also conserved in Bacteroides vulgatus, thereby providing new mechanistic insights into the role of SGBPs in the metabolism of dietary fiber of importance for gut health. Various in vitro analyses, including saturation transfer difference nuclear magnetic resonance (STD-NMR) spectroscopy, revealed that the SusD-like protein cannot bind to the cognate substrate of the XOS PUL, although its presence is essential for the PUL to function. Analysis of the crystal structure of the SusD-like protein reveals an unfolded binding surface and the absence or inappropriate orientation of several key residues compared with other known SusD-like structures. These results highlight the critical role of the SusD-like protein in the transport of oligosaccharides and provide fundamental knowledge about the structure-function of SusC/D-like transporters, revealing that the binding specificity of SusD-like SGBPs does not necessarily reflect the uptake specificity of the transporter. IMPORTANCE The metabolization of dietary fiber is a crucial function for many gut bacteria, especially Bacteroidetes, which are particularly well adapted for recognizing, binding, transporting, and degrading glycosides. In this study, we report the functional and structural characterization of a SusD-like protein involved in xylooligosaccharide utilization by an uncultured gut Bacteroides strain. We demonstrate that while this protein is structurally similar to many canonical Bacteroidetes surface glycan-binding proteins, it cannot bind the substrate taken up by the cognate SusC-like transporter. This lack of binding might be explained by the absence of several key residues known to be involved in oligosaccharide binding and/or the possible necessity of the SusC-like protein to be present to create a cooperative binding site. The term “surface glycan-binding proteins” generally used for SusD-like proteins is thus not generic. Overall, this study allowed us to revisit the concept of glycoside utilization by Bacteroidetes, in particular those strains that feed on the short fibers naturally present in some dietary compounds or on the leftovers of other microbes.
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65
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Stentz R, Jones E, Juodeikis R, Wegmann U, Guirro M, Goldson AJ, Brion A, Booth C, Sudhakar P, Brown IR, Korcsmáros T, Carding SR. The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors. Appl Environ Microbiol 2022; 88:e0053322. [PMID: 35916501 PMCID: PMC9397113 DOI: 10.1128/aem.00533-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Bacterial extracellular vesicles (BEVs) released from both Gram-negative and Gram-positive bacteria provide an effective means of communication and trafficking of cell signaling molecules. In the gastrointestinal tract (GIT) BEVs produced by members of the intestinal microbiota can impact host health by mediating microbe-host cell interactions. A major unresolved question, however, is what factors influence the composition of BEV proteins and whether the host influences protein packaging into BEVs and secretion into the GIT. To address this, we have analyzed the proteome of BEVs produced by the major human gut symbiont Bacteroides thetaiotaomicron both in vitro and in vivo in the murine GIT in order to identify proteins specifically enriched in BEVs produced in vivo. We identified 113 proteins enriched in BEVs produced in vivo, the majority (62/113) of which accumulated in BEVs in the absence of any changes in their expression by the parental cells. Among these selectively enriched proteins, we identified dipeptidyl peptidases and an asparaginase and confirmed their increased activity in BEVs produced in vivo. We also showed that intact BEVs are capable of degrading bile acids via a bile salt hydrolase. Collectively these findings provide additional evidence for the dynamic interplay of host-microbe interactions in the GIT and the existence of an active mechanism to drive and enrich a selected group of proteins for secretion into BEVs in the GIT. IMPORTANCE The gastrointestinal tract (GIT) harbors a complex community of microbes termed the microbiota that plays a role in maintaining the host's health and wellbeing. How this comes about and the nature of microbe-host cell interactions in the GIT is still unclear. Recently, nanosized vesicles naturally produced by bacterial constituents of the microbiota have been shown to influence responses of different host cells although the molecular basis and identity of vesicle-born bacterial proteins that mediate these interactions is unclear. We show here that bacterial extracellular vesicles (BEVs) produced by the human symbiont Bacteroides thetaiotaomicron in the GIT are enriched in a set of proteins and enzymes, including dipeptidyl peptidases, an asparaginase and a bile salt hydrolase that can influence host cell biosynthetic pathways. Our results provide new insights into the molecular basis of microbiota-host interactions that are central to maintaining GIT homeostasis and health.
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Affiliation(s)
- Régis Stentz
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Emily Jones
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Rokas Juodeikis
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
| | - Udo Wegmann
- School of Chemistry, University East Anglia, Norwich, United Kingdom
| | - Maria Guirro
- Biochemistry and Biotechnology Department, Nutrigenomics Research Group, Universitat Rovira i Virgili, Tarragona, Spain
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Andrew J. Goldson
- Core Science Resources Quadram Institute Bioscience, Norwich, United Kingdom
| | - Arlaine Brion
- Core Science Resources Quadram Institute Bioscience, Norwich, United Kingdom
| | - Catherine Booth
- Core Science Resources Quadram Institute Bioscience, Norwich, United Kingdom
| | - Padhmanand Sudhakar
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Earlham Institute, Norwich, United Kingdom
- Department of Chronic Diseases, Metabolism and Ageing, TARGID, KU Leuven, Leuven, Belgium
| | - Ian R. Brown
- School of Biosciences, University of Kent, Canterbury, United Kingdom
| | - Tamás Korcsmáros
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Earlham Institute, Norwich, United Kingdom
| | - Simon R. Carding
- Gut Microbes and Health Research Programme, Quadram Institute Bioscience, Norwich, United Kingdom
- Norwich Medical School, University East Anglia, Norwich, United Kingdom
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66
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Flavobacterium litorale sp. nov., isolated from red alga. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-negative and rod-shaped bacterial strain (WSW3-B6T) was isolated from red alga collected from the West Sea, Republic of Korea. Cells of strain WSW3-B6T were non-motile, aerobic and produced slightly yellow and mucoid colonies on marine agar. The strain grew optimally at 23–30 °C, with 0.5–4 % NaCl (w/v) and at pH 6.5–8.5. A phylogenetic analysis of the 16S rRNA gene revealed that strain WSW3-B6T belongs to the genus
Flavobacterium
within the family
Flavobacteriaceae
, having the highest sequence similarity to
Flavobacterium arcticum
SM1502T (96.7%), followed by
Flavobacterium salilacus
subsp.
altitudinum
LaA7.5T (96.2%) and
Flavobacterium salilacus
subsp.
salilacus
SaA2.12T (96.2%). The complete sequence of a circular chromosome of strain WSW3-B6T determined by combination of Oxford Nanopore and Illumina platforms comprised a total 2 725 095 bp with G+C content of 37.1 mol%. A comparative analysis based on the whole genome also showed the distinctiveness of strain WSW3-B6T. The average nucleotide identity (ANI) values between strain WSW3-B6T and the closest strains
F. arcticum
SM1502T,
F. salilacus
subsp.
altitudinum
LaA7.5T and
F. salilacus
subsp.
salilacus
SaA2.12T were 78.3, 77.8 and 77.7 %, respectively, while the digital DNA–DNA hybridization (dDDH) values between strain WSW3-B6T and the above closely related strains were 21.0, 20.4 and 20.3 %, respectively. Both the ANI and dDDH values supported the creation of a new species in the genus
Flavobacterium
. The major fatty acids (>10 %) were iso-C15 : 0 (19.3 %), C16 : 0 (14.0 %), iso-C17 : 0 3-OH (13.1 %) and C18 : 0 (10.7 %). The polar lipids of strain WSW3-B6T included phosphatidylethanolamine, three unidentified aminolipids and three unidentified lipids. Moreover, MK-6 was the only respiratory quinone. A comparison of the phylogenetic distinctiveness and the unique phenotypic and chemotaxonomic characteristics among strain WSW3-B6T and closely related type strains supported that strain WSW3-B6T (=KCTC 82708T=GDMCC 1.2627T) represents a novel species of the genus
Flavobacterium
, for which the name Flavobacterium litorale sp. nov. is proposed.
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67
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Cui Y, Zhang L, Wang X, Yi Y, Shan Y, Liu B, Zhou Y, Lü X. Roles of intestinal Parabacteroides in human health and diseases. FEMS Microbiol Lett 2022; 369:6659190. [PMID: 35945336 DOI: 10.1093/femsle/fnac072] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 06/09/2022] [Accepted: 08/05/2022] [Indexed: 11/13/2022] Open
Abstract
The stability of gut microbiota is essential for the host health. Parabacteroides spp., core members of the human gut microbiota, have average abundance of 1.27% in the human of 12 populations. Parabacteroides has been recently reported to have a close relationship with host health (E.g., metabolic syndrome, inflammatory bowel disease and obesity). Parabacteroides have the physiological characteristics of carbohydrate metabolism and secreting SCFAs. However, antimicrobial resistance of Parabacteroides to antibiotic (such as clindamycin, moxifloxacin and cefoxitin) should not be ignored. In this review, we primarily focused on Parabacteroides distasoniss, Parabacteroides goldsteinii, Parabacteroides johnsonii and Parabacteroides merdae and discussed their relationships with host disease, diet and the prevention or induction of diseases. P. distasonis and P. goldsteinii may be viewed as the potential next generation probiotics (NGP) candidate due to their protective effects on inflammation and obesity in mice. We also discussed the potential therapeutic application of Parabacteroides spp. in maintaining host-intestine homeostasis.
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Affiliation(s)
- Yanlong Cui
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Leshan Zhang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Wang
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yanglei Yi
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuanyuan Shan
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Bianfang Liu
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Yuan Zhou
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
| | - Xin Lü
- Lab of Bioresources, College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi Province, China
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68
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Vasudeva G, Singh H, Paliwal S, Pinnaka AK. Metagenomics: An Approach for Unraveling the Community Structure and Functional Potential of Activated Sludge of a Common Effluent Treatment Plant. Front Microbiol 2022; 13:933373. [PMID: 35958153 PMCID: PMC9358654 DOI: 10.3389/fmicb.2022.933373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 06/17/2022] [Indexed: 11/23/2022] Open
Abstract
The common effluent treatment plant (CETP) located at Baddi treats the industrial effluent from various industries, leading to the pooling of a diverse range of substrates and metabolites. The nutrient loading and its availability decide the balance of the microbial community and its diversity. The samples thus collected from the activated sludge (BS14) of CETP and Sirsa river (SR1) from the vicinity of CETP effluent discharge were processed for the whole metagenome analysis to reveal the microbial community and its functional potential. The taxonomic classification of the BS14 sample showed the dominance of the bacterial community with 96% of abundance, whereas the SR1 was populated by eukaryotes representing 50.4% of the community of SR1. The bacterial community of SR1 was constituted of 47.2%. The functional analysis of BS14 and SR1 with GhostKOALA against the KEGG database assigned 43.7% and 27.8% of the open reading frames (ORFs) with functions. It revealed the xenobiotic degradation modules with complete pathways along with resistance against the beta-lactams. The analysis with the comprehensive antibiotic resistance database (CARD) revealed 33 and 32 unique types of antimicrobial resistance in BS14 and SR1, respectively. Both the samples were dominated by the beta-lactam resistance genes. The carbohydrate-active enzyme (CAZy) database assigned a total of 6,611 and 2,941 active enzymes to BS14 and SR1, respectively. In contrast, the glycosyl hydrolases (GH) and glycosyltransferases (GT) class of enzymes were found to be abundant in both the samples as compared with polysaccharide lyases (PL), auxiliary activities (AA), carbohydrate esterases (CE), and carbohydrate-binding module (CBM).
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69
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Kondrotaite Z, Valk LC, Petriglieri F, Singleton C, Nierychlo M, Dueholm MKD, Nielsen PH. Diversity and Ecophysiology of the Genus OLB8 and Other Abundant Uncultured Saprospiraceae Genera in Global Wastewater Treatment Systems. Front Microbiol 2022; 13:917553. [PMID: 35875537 PMCID: PMC9304909 DOI: 10.3389/fmicb.2022.917553] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
The Saprospiraceae family within the phylum Bacteroidota is commonly present and highly abundant in wastewater treatment plants (WWTPs) worldwide, but little is known about its role. In this study, we used MiDAS 4 global survey with samples from 30 countries to analyze the abundance and distribution of members of Saprospiraceae. Phylogenomics were used to delineate five new genera from a set of 31 high-quality metagenome-assembled genomes from Danish WWTPs. Newly designed probes for fluorescence in situ hybridization (FISH) revealed rod-shaped morphologies for all genera analyzed, including OLB8, present mostly inside the activated sludge flocs. The genomes revealed potential metabolic capabilities for the degradation of polysaccharides, proteins, and other complex molecules; partial denitrification; and storage of intracellular polymers (glycogen, polyphosphate, and polyhydroxyalkanoates). FISH in combination with Raman microspectroscopy confirmed the presence of intracellular glycogen in Candidatus Brachybacter, Candidatus Parvibacillus calidus (both from the former genus OLB8), and Candidatus Opimibacter, and the presence of polyhydroxyalkanoates in Candidatus Defluviibacterium haderslevense and Candidatus Vicinibacter. These results provide the first overview of the most abundant novel Saprospiraceae genera present in WWTPs across the world and their potential involvement in nutrient removal and the degradation of macromolecules.
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Affiliation(s)
| | | | | | | | | | | | - Per H. Nielsen
- Department of Chemistry and Bioscience, Center of Microbial Communities, Aalborg University, Aalborg, Denmark
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70
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Han ND, Cheng J, Delannoy-Bruno O, Webber D, Terrapon N, Henrissat B, Rodionov DA, Arzamasov AA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Desai C, Marion S, Barratt MJ, Heath AC, Gordon JI. Microbial liberation of N-methylserotonin from orange fiber in gnotobiotic mice and humans. Cell 2022; 185:2495-2509.e11. [PMID: 35764090 DOI: 10.1016/j.cell.2022.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/23/2021] [Accepted: 06/03/2022] [Indexed: 12/13/2022]
Abstract
Plant fibers in byproduct streams produced by non-harsh food processing methods represent biorepositories of diverse, naturally occurring, and physiologically active biomolecules. To demonstrate one approach for their characterization, mass spectrometry of intestinal contents from gnotobiotic mice, plus in vitro studies, revealed liberation of N-methylserotonin from orange fibers by human gut microbiota members including Bacteroides ovatus. Functional genomic analyses of B. ovatus strains grown under permissive and non-permissive N-methylserotonin "mining" conditions revealed polysaccharide utilization loci that target pectins whose expression correlate with strain-specific liberation of this compound. N-methylserotonin, orally administered to germ-free mice, reduced adiposity, altered liver glycogenesis, shortened gut transit time, and changed expression of genes that regulate circadian rhythm in the liver and colon. In human studies, dose-dependent, orange-fiber-specific fecal accumulation of N-methylserotonin positively correlated with levels of microbiome genes encoding enzymes that digest pectic glycans. Identifying this type of microbial mining activity has potential therapeutic implications.
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Affiliation(s)
- Nathan D Han
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Jiye Cheng
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Omar Delannoy-Bruno
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Daniel Webber
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, 13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, 13288 Marseille, France; Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Aleksandr A Arzamasov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | | | | | - Chandani Desai
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA
| | - Stacey Marion
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Michael J Barratt
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jeffrey I Gordon
- The Edison Family Center for Genome Sciences and Systems Biology, St. Louis, MO 63110, USA; Center for Gut Microbiome and Nutrition Research, St. Louis, MO 63110, USA.
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71
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Qu L, Cai R, Hu Z, Wang H. Metagenomic assemblage genomes analyses reveal the polysaccharides hydrolyzing potential of marine group II euryarchaea. ENVIRONMENTAL RESEARCH 2022; 209:112865. [PMID: 35120891 DOI: 10.1016/j.envres.2022.112865] [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: 10/17/2021] [Revised: 01/02/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Marine group II euryarchaea (MGII) dominates the planktonic archaeal community in global surface seawater and is associated to particulate organic matters mainly composed of polysaccharides. However, the polysaccharides metabolism of MGII euryarchaea is unclear. In this study, the distribution and polysaccharides metabolism potential of MGII euryarchaea in the estuary were investigated. High-throughput sequencing of 16S rRNA genes showed that MGII euryarchaea was the predominant archaeal group in the Pearl River Estuary (PRE), and the relative abundance of MGII euryarchaea in particle-attached fraction was higher than that in free-living fractions. A total of 19 metagenome-assembled genomes (MAGs) were successfully reconstructed from metagenomic data, of which 10 MAGs were grouped as MGII euryarchaea according to phylogenomic analysis. Genes encoding a variety of carbohydrate-active enzymes (CAZymes) were found in MAGs/genomes of MGII euryarchaea. These CAZymes annotated in MAGs were capable of hydrolyzing many polysaccharides, including α-glucans, β-glucans, xylans, nitrogen-containing polysaccharides, and some insoluble galactans. The results also indicated that MGII euryarchaea has some unique enzymes that can hydrolyze starch, β-1,3-glucans, complex xylans, carrageenan, and agarose. Collectively, our results demonstrated that MGII euryarchaea has great polysaccharides hydrolysis potential and could play an important role in the carbon cycle of marine ecosystem.
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Affiliation(s)
- Liping Qu
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Runlin Cai
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Zhong Hu
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China
| | - Hui Wang
- Biology Department and Institute of Marine Sciences, College of Science, Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, 511458, China.
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72
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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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73
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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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74
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Functional exploration of the glycoside hydrolase family GH113. PLoS One 2022; 17:e0267509. [PMID: 35452491 PMCID: PMC9032380 DOI: 10.1371/journal.pone.0267509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/08/2022] [Indexed: 12/02/2022] Open
Abstract
β-Mannans are a heterogeneous group of polysaccharides with a common main chain of β-1,4-linked mannopyranoside residues. The cleavage of β-mannan chains is catalyzed by glycoside hydrolases called β-mannanases. In the CAZy database, β-mannanases are grouped by sequence similarity in families GH5, GH26, GH113 and GH134. Family GH113 has been under-explored so far with six enzymes characterized, all from the Firmicutes phylum. We undertook the functional characterization of 14 enzymes from a selection of 31 covering the diversity of the family GH113. Our observations suggest that GH113 is a family with specificity towards mannans, with variations in the product profiles and modes of action. We were able to assign mannanase and mannosidase activities to four out of the five clades of the family, increasing by 200% the number of characterized GH113 members, and expanding the toolbox for fine-tuning of mannooligosaccharides.
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75
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Elucidating Sequence and Structural Determinants of Carbohydrate Esterases for Complete Deacetylation of Substituted Xylans. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092655. [PMID: 35566004 PMCID: PMC9105624 DOI: 10.3390/molecules27092655] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/07/2022] [Accepted: 04/14/2022] [Indexed: 11/26/2022]
Abstract
Acetylated glucuronoxylan is one of the most common types of hemicellulose in nature. The structure is formed by a β-(1→4)-linked D-xylopyranosyl (Xylp) backbone that can be substituted with an acetyl group at O-2 and O-3 positions, and α-(1→2)-linked 4-O-methylglucopyranosyluronic acid (MeGlcpA). Acetyl xylan esterases (AcXE) that target mono- or doubly acetylated Xylp are well characterized; however, the previously studied AcXE from Flavobacterium johnsoniae (FjoAcXE) was the first to remove the acetyl group from 2-O-MeGlcpA-3-O-acetyl-substituted Xylp units, yet structural characteristics of these enzymes remain unspecified. Here, six homologs of FjoAcXE were produced and three crystal structures of the enzymes were solved. Two of them are complex structures, one with bound MeGlcpA and another with acetate. All homologs were confirmed to release acetate from 2-O-MeGlcpA-3-O-acetyl-substituted xylan, and the crystal structures point to key structural elements that might serve as defining features of this unclassified carbohydrate esterase family. Enzymes comprised two domains: N-terminal CBM domain and a C-terminal SGNH domain. In FjoAcXE and all studied homologs, the sequence motif around the catalytic serine is Gly-Asn-Ser-Ile (GNSI), which differs from other SGNH hydrolases. Binding by the MeGlcpA-Xylp ligand is directed by positively charged and highly conserved residues at the interface of the CBM and SGNH domains of the enzyme.
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76
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Wang Z, Tauzin AS, Laville E, Potocki-Veronese G. Identification of Glycoside Transporters From the Human Gut Microbiome. Front Microbiol 2022; 13:816462. [PMID: 35401468 PMCID: PMC8990778 DOI: 10.3389/fmicb.2022.816462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/14/2022] [Indexed: 11/17/2022] Open
Abstract
Transport is a crucial step in the metabolism of glycosides by bacteria, which is itself key for microbiota function and equilibrium. However, most transport proteins are function-unknown or only predicted, limiting our understanding of how bacteria utilize glycosides. Here, we present an activity-based screening method to identify functional glycoside transporters from microbiomes. The method is based on the co-expression in Escherichia coli of genes encoding transporters and carbohydrate-active enzymes (CAZymes) from metagenomic polysaccharide utilization loci (PULs) cloned in fosmids. To establish the proof of concept of the methodology, we used two different metagenomic libraries derived from human gut microbiota to select 18 E. coli clones whose metagenomic sequence contained at least one putative glycoside transporter and one functional CAZyme, identified by screening for various glycoside-hydrolase activities. Growth tests were performed on plant-derived glycosides, which are the target substrates of the CAZymes identified in each PUL. This led to the identification of 10 clones that are able to utilize oligosaccharides as sole carbon sources, thanks to the production of transporters from the PTS, ABC, MFS, and SusCD families. Six of the 10 hit clones contain only one transporter, providing direct experimental evidence that these transporters are functional. In the six cases where two transporters are present in the sequence of a clone, the transporters’ function can be predicted from the flanking CAZymes or from similarity with transporters characterized previously, which facilitates further functional characterization. The results expand the understanding of how glycosides are selectively metabolized by bacteria and offers a new approach to screening for glycoside-transporter specificity toward oligosaccharides with defined structures.
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Affiliation(s)
- Zhi Wang
- TBI, CNRS, INRA, INSAT, Université de Toulouse, Toulouse, France
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77
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Ostrowski MP, La Rosa SL, Kunath BJ, Robertson A, Pereira G, Hagen LH, Varghese NJ, Qiu L, Yao T, Flint G, Li J, McDonald SP, Buttner D, Pudlo NA, Schnizlein MK, Young VB, Brumer H, Schmidt TM, Terrapon N, Lombard V, Henrissat B, Hamaker B, Eloe-Fadrosh EA, Tripathi A, Pope PB, Martens EC. Mechanistic insights into consumption of the food additive xanthan gum by the human gut microbiota. Nat Microbiol 2022; 7:556-569. [PMID: 35365790 DOI: 10.1038/s41564-022-01093-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
Processed foods often include food additives such as xanthan gum, a complex polysaccharide with unique rheological properties, that has established widespread use as a stabilizer and thickening agent. Xanthan gum's chemical structure is distinct from those of host and dietary polysaccharides that are more commonly expected to transit the gastrointestinal tract, and little is known about its direct interaction with the gut microbiota, which plays a central role in digestion of other dietary fibre polysaccharides. Here we show that the ability to digest xanthan gum is common in human gut microbiomes from industrialized countries and appears contingent on a single uncultured bacterium in the family Ruminococcaceae. Our data reveal that this primary degrader cleaves the xanthan gum backbone before processing the released oligosaccharides using additional enzymes. Some individuals harbour Bacteroides intestinalis that is incapable of consuming polymeric xanthan gum but grows on oligosaccharide products generated by the Ruminococcaceae. Feeding xanthan gum to germfree mice colonized with a human microbiota containing the uncultured Ruminococcaceae supports the idea that the additive xanthan gum can drive expansion of the primary degrader Ruminococcaceae, along with exogenously introduced B. intestinalis. Our work demonstrates the existence of a potential xanthan gum food chain involving at least two members of different phyla of gut bacteria and provides an initial framework for understanding how widespread consumption of a recently introduced food additive influences human microbiomes.
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Affiliation(s)
- Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway.,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Benoit J Kunath
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Andrew Robertson
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Pereira
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Live H Hagen
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | | | - Ling Qiu
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Tianming Yao
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | - Gabrielle Flint
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - James Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sean P McDonald
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Duna Buttner
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas A Pudlo
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,Department of Internal Medicine, Infectious Diseases Division, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Thomas M Schmidt
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Vincent Lombard
- Centre National de la Recherche Scientifique, Aix-Marseille Univ, Marseille, France.,Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Bernard Henrissat
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.,Technical University of Denmark, DTU Bioengineering, Lyngby, Denmark
| | - Bruce Hamaker
- Department of Food Science and Whistler Center for Carbohydrate Research, Purdue University, West Lafayette, IN, USA
| | | | - Ashootosh Tripathi
- Life Sciences Institute: Natural Products Discovery Core, University of Michigan, Ann Arbor, MI, USA
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway. .,Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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78
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Wardman JF, Bains RK, Rahfeld P, Withers SG. Carbohydrate-active enzymes (CAZymes) in the gut microbiome. Nat Rev Microbiol 2022; 20:542-556. [PMID: 35347288 DOI: 10.1038/s41579-022-00712-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
Abstract
The 1013-1014 microorganisms present in the human gut (collectively known as the human gut microbiota) dedicate substantial percentages of their genomes to the degradation and uptake of carbohydrates, indicating the importance of this class of molecules. Carbohydrates function not only as a carbon source for these bacteria but also as a means of attachment to the host, and a barrier to infection of the host. In this Review, we focus on the diversity of carbohydrate-active enzymes (CAZymes), how gut microorganisms use them for carbohydrate degradation, the different chemical mechanisms of these CAZymes and the roles that these microorganisms and their CAZymes have in human health and disease. We also highlight examples of how enzymes from this treasure trove have been used in manipulation of the microbiota for improved health and treatment of disease, in remodelling the glycans on biopharmaceuticals and in the potential production of universal O-type donor blood.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rajneesh K Bains
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. .,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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79
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McGregor NGS, Overkleeft HS, Davies GJ. Detecting and identifying glycoside hydrolases using cyclophellitol-derived activity-based probes. Methods Enzymol 2022; 664:103-134. [PMID: 35331370 DOI: 10.1016/bs.mie.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ability to detect active enzymes in a complex mixture of folded proteins (e.g., secretome, cell lysate) generally relies on observations of catalytic ability, necessitating the development of an activity assay that is compatible with the sample and selective for the enzyme(s) of interest. Deconvolution of the contributions of different enzymes to an observed catalytic ability further necessitates an often-challenging protein separation. The advent of broadly reactive activity-based probes (ABPs) for retaining glycoside hydrolases (GHs) has enabled an alternative, often complementary, assay for active GHs. Using activity-based protein profiling (ABPP) techniques, many retaining glycoside hydrolases can be separated, detected, and identified with high sensitivity and selectivity. This chapter outlines ABPP methods for the detection and identification of retaining glycoside hydrolases from microbial sources, including protein sample preparation from bacterial lysates and fungal secretomes, enzyme labeling and detection via fluorescence, and enzyme identification using affinity-based enrichment coupled to peptide sequencing following isobaric labeling.
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Affiliation(s)
- Nicholas G S McGregor
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom
| | | | - Gideon J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York, United Kingdom.
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80
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Singh RP, Bhaiyya R, Thakur R, Niharika J, Singh C, Latousakis D, Saalbach G, Nepogodiev SA, Singh P, Sharma SC, Sengupta S, Juge N, Field RA. Biochemical Basis of Xylooligosaccharide Utilisation by Gut Bacteria. Int J Mol Sci 2022; 23:2992. [PMID: 35328413 PMCID: PMC8954004 DOI: 10.3390/ijms23062992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 01/27/2023] Open
Abstract
Xylan is one of the major structural components of the plant cell wall. Xylan present in the human diet reaches the large intestine undigested and becomes a substrate to species of the gut microbiota. Here, we characterised the capacity of Limosilactobacillus reuteri and Blautia producta strains to utilise xylan derivatives. We showed that L. reuteri ATCC 53608 and B. producta ATCC 27340 produced β-D-xylosidases, enabling growth on xylooligosaccharide (XOS). The recombinant enzymes were highly active on artificial (p-nitrophenyl β-D-xylopyranoside) and natural (xylobiose, xylotriose, and xylotetraose) substrates, and showed transxylosylation activity and tolerance to xylose inhibition. The enzymes belong to glycoside hydrolase family 120 with Asp as nucleophile and Glu as proton donor, as shown by homology modelling and confirmed by site-directed mutagenesis. In silico analysis revealed that these enzymes were part of a gene cluster in L. reuteri but not in Blautia strains, and quantitative proteomics identified other enzymes and transporters involved in B. producta XOS utilisation. Based on these findings, we proposed a model for an XOS metabolism pathway in L. reuteri and B. producta strains. Together with phylogenetic analyses, the data also revealed the extended xylanolytic potential of the gut microbiota.
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Affiliation(s)
- Ravindra Pal Singh
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute (NABI), SAS Nagar 140306, India; (R.B.); (R.T.); (J.N.); (C.S.)
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK; (G.S.); (S.A.N.)
| | - Raja Bhaiyya
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute (NABI), SAS Nagar 140306, India; (R.B.); (R.T.); (J.N.); (C.S.)
| | - Raksha Thakur
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute (NABI), SAS Nagar 140306, India; (R.B.); (R.T.); (J.N.); (C.S.)
| | - Jayashree Niharika
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute (NABI), SAS Nagar 140306, India; (R.B.); (R.T.); (J.N.); (C.S.)
| | - Chandrajeet Singh
- Division of Food and Nutritional Biotechnology, National Agri-Food Biotechnology Institute (NABI), SAS Nagar 140306, India; (R.B.); (R.T.); (J.N.); (C.S.)
| | - Dimitrios Latousakis
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (D.L.); (N.J.)
| | - Gerhard Saalbach
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK; (G.S.); (S.A.N.)
| | - Sergey A. Nepogodiev
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK; (G.S.); (S.A.N.)
| | - Praveen Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India; (P.S.); (S.S.)
| | - Sukesh Chander Sharma
- Department of Biochemistry, South Campus, Panjab University, Chandigarh 160014, India;
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India; (P.S.); (S.S.)
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Programme, Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, UK; (D.L.); (N.J.)
| | - Robert A. Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR47UH, UK; (G.S.); (S.A.N.)
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81
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Abstract
Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/Bacteroides xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multilocus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors. IMPORTANCE Nonharmful bacteria are the primary microbial symbionts that inhabit the human gastrointestinal tract. These bacteria play many beneficial roles and in some cases can modify disease states, making it important to understand which nutrients sustain specific lineages. This knowledge will in turn lead to strategies to intentionally manipulate the gut microbial ecosystem. We designed a scalable, high-throughput platform for measuring the ability of gut bacteria to utilize polysaccharides, of which many are derived from dietary fiber sources that can be manipulated easily. Our results provide paths to expand phenotypic surveys of more diverse gut bacteria to understand their functions and also to leverage dietary fibers to alter the physiology of the gut microbial community.
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82
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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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83
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Cabral L, Persinoti GF, Paixão DAA, Martins MP, Morais MAB, Chinaglia M, Domingues MN, Sforca ML, Pirolla RAS, Generoso WC, Santos CA, Maciel LF, Terrapon N, Lombard V, Henrissat B, Murakami MT. Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides. Nat Commun 2022; 13:629. [PMID: 35110564 PMCID: PMC8810776 DOI: 10.1038/s41467-022-28310-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 01/14/2022] [Indexed: 12/12/2022] Open
Abstract
The largest living rodent, capybara, can efficiently depolymerize and utilize lignocellulosic biomass through microbial symbiotic mechanisms yet elusive. Herein, we elucidate the microbial community composition, enzymatic systems and metabolic pathways involved in the conversion of dietary fibers into short-chain fatty acids, a main energy source for the host. In this microbiota, the unconventional enzymatic machinery from Fibrobacteres seems to drive cellulose degradation, whereas a diverse set of carbohydrate-active enzymes from Bacteroidetes, organized in polysaccharide utilization loci, are accounted to tackle complex hemicelluloses typically found in gramineous and aquatic plants. Exploring the genetic potential of this community, we discover a glycoside hydrolase family of β-galactosidases (named as GH173), and a carbohydrate-binding module family (named as CBM89) involved in xylan binding that establishes an unprecedented three-dimensional fold among associated modules to carbohydrate-active enzymes. Together, these results demonstrate how the capybara gut microbiota orchestrates the depolymerization and utilization of plant fibers, representing an untapped reservoir of enzymatic mechanisms to overcome the lignocellulose recalcitrance, a central challenge toward a sustainable and bio-based economy. Here, Cabral et al., perform a multi-omics analysis of the gut microbiome of capybara, the largest living rodent, unveiling enzymatic mechanisms for the breakdown of lignocellulosic biomass, and report two undescribed families of carbohydrate-active enzymes.
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Affiliation(s)
- Lucelia Cabral
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Gabriela F Persinoti
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
| | - Douglas A A Paixão
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Marcele P Martins
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariana A B Morais
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mariana Chinaglia
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.,Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - Mariane N Domingues
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Mauricio L Sforca
- Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Renan A S Pirolla
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Wesley C Generoso
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Clelton A Santos
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Lucas F Maciel
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil
| | - Nicolas Terrapon
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Vincent Lombard
- The Institut National de la Recherche Agronomique, USC 1408 AFMB, 13288, Marseille, France.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine (DTU Bioengineering), Technical University of Denmark, 2800 Kgs, Lyngby, Denmark.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mario T Murakami
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, SP, Brazil.
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84
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Malgas S, Thoresen M, Moses V, Prinsloo E, Susan van Dyk J, Pletschke BI. Analysis of the galactomannan binding ability of β-mannosidases, BtMan2A and CmMan5A, regarding their activity and synergism with a β-mannanase. Comput Struct Biotechnol J 2022; 20:3140-3150. [PMID: 35782739 PMCID: PMC9232400 DOI: 10.1016/j.csbj.2022.06.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/14/2022] [Accepted: 06/14/2022] [Indexed: 11/28/2022] Open
Abstract
BtMan2A preferred short manno-oligomers, while CmMan5A preferred longer ones; DP >2. BtMan2A displayed stronger irreversible binding to galactomannan than CmMan5A. BtMan2A binding to galactomannan did not affect its activity, while CmMan5A lost activity. BtMan2A binding was pH-dependent, with increased binding ability at lower pH. CmMan5A synergised with CcManA, while BtMan2A did not – even though the enzyme was active. High loadings of BtMan2A abolished CcManA activity; at protein ratios ≥ 5:1.
Both β-mannanases and β-mannosidases are required for mannan-backbone degradation into mannose. In this study, two β-mannosidases of glycoside hydrolase (GH) families 2 (BtMan2A) and 5 (CmMan5A) were evaluated for their substrate specificities and galactomannan binding ability. BtMan2A preferred short manno-oligomers, while CmMan5A preferred longer ones; DP >2, and galactomannans. BtMan2A displayed irreversible galactomannan binding, which was pH-dependent, with higher binding observed at low pH, while CmMan5A had limited binding. Docking and molecular dynamics (MD) simulations showed that BtMan2A galactomannan binding was stronger under acidic conditions (-8.4 kcal/mol) than in a neutral environment (-7.6 kcal/mol), and the galactomannan ligand was more unstable under neutral conditions than acidic conditions. Qualitative surface plasmon resonance (SPR) experimentally confirmed the reduced binding capacity of BtMan2A at pH 7. Finally, synergistic β-mannanase to β-mannosidase (BtMan2A or CmMan5A) ratios required for maximal galactomannan hydrolysis were determined. All CcManA to CmMan5A combinations were synergistic (≈1.2-fold), while combinations of CcManA with BtMan2A (≈1.0-fold) yielded no hydrolysis improvement. In conclusion, the low specific activity of BtMan2A towards long and galactose-containing oligomers and its non-catalytic galactomannan binding ability led to no synergy with the mannanase, making GH2 mannosidases ineffective for use in cocktails for mannan degradation.
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Affiliation(s)
- Samkelo Malgas
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, Eastern Cape 6140, South Africa
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Gauteng 0028, South Africa
- Corresponding author at: Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, Gauteng 0028, South Africa.
| | - Mariska Thoresen
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, Eastern Cape 6140, South Africa
| | - Vuyani Moses
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, Eastern Cape 6140, South Africa
| | - Earl Prinsloo
- Biotechnology Innovation Centre, Rhodes University, Makhanda, Eastern Cape 6140, South Africa
| | - J. Susan van Dyk
- Forest Products Biotechnology, University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T1Z4, Canada
| | - Brett I. Pletschke
- Enzyme Science Programme (ESP), Department of Biochemistry and Microbiology, Rhodes University, Makhanda, Eastern Cape 6140, South Africa
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85
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Zerva A, Pentari C, Ferousi C, Nikolaivits E, Karnaouri A, Topakas E. Recent advances on key enzymatic activities for the utilisation of lignocellulosic biomass. BIORESOURCE TECHNOLOGY 2021; 342:126058. [PMID: 34597805 DOI: 10.1016/j.biortech.2021.126058] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
The field of enzymatic degradation of lignocellulose is actively growing and the recent updates of the last few years indicate that there is still much to learn. The growing number of protein sequences with unknown function in microbial genomes indicates that there is still much to learn on the mechanisms of lignocellulose degradation. In this review, a summary of the progress in the field is presented, including recent discoveries on the nature of the structural polysaccharides, new technologies for the discovery and functional annotation of gene sequences including omics technologies, and the novel lignocellulose-acting enzymes described. Novel enzymatic activities and enzyme families as well as accessory enzymes and their synergistic relationships regarding biomass breakdown are described. Moreover, it is shown that all the valuable knowledge of the enzymatic decomposition of plant biomass polymers can be employed towards the decomposition and upgrading of synthetic polymers, such as plastics.
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Affiliation(s)
- Anastasia Zerva
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Pentari
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Christina Ferousi
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efstratios Nikolaivits
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Anthi Karnaouri
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Evangelos Topakas
- Industrial Biotechnology & Biocatalysis Group, Biotechnology Laboratory, School of Chemical Engineering, National Technical University of Athens, Athens, Greece; Biochemical Process Engineering, Chemical Engineering, Department of Civil, Environmental and Natural Resources Engineering, Luleå University of Technology, Luleå, Sweden.
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86
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Golisch B, Lei Z, Tamura K, Brumer H. Configured for the Human Gut Microbiota: Molecular Mechanisms of Dietary β-Glucan Utilization. ACS Chem Biol 2021; 16:2087-2102. [PMID: 34709792 DOI: 10.1021/acschembio.1c00563] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The β-glucans are a disparate group of structurally diverse polysaccharides, whose members are widespread in human diets as components of the cell walls of plants, algae, and fungi (including yeasts), and as bacterial exopolysaccharides. Individual β-glucans from these sources have long been associated with positive effects on human health through metabolic and immunological effects. Remarkably, the β-configured glucosidic linkages that define these polysaccharides render them inaccessible to the limited repertoire of digestive enzymes encoded by the human genome. As a result, the various β-glucans become fodder for the human gut microbiota (HGM) in the lower gastrointestinal tract, where they influence community composition and metabolic output, including fermentation to short chain fatty acids (SCFAs). Only recently, however, have the specific molecular systems that enable the utilization of β-glucans by select members of the HGM been fully elucidated by combined genetic, biochemical, and structural biological approaches. In the context of β-glucan structures and their effects on human nutrition and health, we summarize here the functional characterization of individual polysaccharide utilization loci (PULs) responsible for the saccharification of mixed-linkage β(1→3)/β(1→4)-glucans, β(1→6)-glucans, β(1→3)-glucans, β(1→2)-glucans, and xyloglucans in symbiotic human gut bacteria. These exemplar PULs serve as well-defined biomarkers for the prediction of β-glucan metabolic capability in individual bacterial taxa and across the global human population.
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87
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Linares-Pastén JA, Hero JS, Pisa JH, Teixeira C, Nyman M, Adlercreutz P, Martinez MA, Karlsson EN. Novel xylan-degrading enzymes from polysaccharide utilizing loci of Prevotella copri DSM18205. Glycobiology 2021; 31:1330-1349. [PMID: 34142143 PMCID: PMC8631079 DOI: 10.1093/glycob/cwab056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/20/2021] [Accepted: 06/09/2021] [Indexed: 11/24/2022] Open
Abstract
Prevotella copri is a bacterium that can be found in the human gastrointestinal tract (GIT). The role of P. copri in the GIT is unclear, and elevated numbers of the microbe have been reported both in dietary fiber-induced improvement in glucose metabolism but also in conjunction with certain inflammatory conditions. These findings raised our interest in investigating the possibility of P. copri to grow on xylan, and identify the enzyme systems playing a role in digestion of xylan-based dietary fibers. Two xylan degrading polysaccharide utilizing loci (PUL10 and 15) were found in the genome, with three and eight glycoside hydrolase (GH) -encoding genes, respectively. Three of them were successfully produced in Escherichia coli: One extracellular enzyme from GH43 (subfamily 12, in PUL10, 60 kDa) and two enzymes from PUL15, one extracellular GH10 (41 kDa), and one intracellular GH43 (subfamily 137 kDa). Based on our results, we propose that in PUL15, GH10 (1) is an extracellular endo-1,4-β-xylanase, that hydrolazes mainly glucuronosylated xylan polymers to xylooligosaccharides (XOS); while, GH43_1 in the same PUL, is an intracellular β-xylosidase, catalyzing complete hydrolysis of the XOS to xylose. In PUL10, the characterized GH43_12 is an arabinofuranosidase, with a role in degradation of arabinoxylan, catalyzing removal of arabinose-residues on xylan.
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Affiliation(s)
| | - Johan Sebastian Hero
- Planta Piloto de Procesos Industriales Microbiológicos
PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB
San Miguel de Tucumán, Argentina
| | - José Horacio Pisa
- Planta Piloto de Procesos Industriales Microbiológicos
PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB
San Miguel de Tucumán, Argentina
| | - Cristina Teixeira
- Biotechnology, Department of Chemistry,
Lund University, P.O. Box 124, 221 00 Lund,
Sweden
| | - Margareta Nyman
- Department of Food Technology, Engineering and
Nutrition, Lund University, P.O. Box 124, SE-221
00 Lund, Sweden
| | - Patrick Adlercreutz
- Biotechnology, Department of Chemistry,
Lund University, P.O. Box 124, 221 00 Lund,
Sweden
| | - M Alejandra Martinez
- Planta Piloto de Procesos Industriales Microbiológicos
PROIMI-CONICET, Av. Belgrano y Pasaje Caseros, T4001 MVB
San Miguel de Tucumán, Argentina
- Facultad de Ciencias Exactas y
Tecnología, UNT. Av. Independencia 1800, San Miguel de
Tucumán 4000, Argentina
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry,
Lund University, P.O. Box 124, 221 00 Lund,
Sweden
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88
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Tegl G, Rahfeld P, Ostmann K, Hanson J, Withers SG. Discovery of β- N-acetylglucosaminidases from screening metagenomic libraries and their use as thioglycoligase mutants. Org Biomol Chem 2021; 19:9068-9075. [PMID: 34622263 DOI: 10.1039/d1ob01246k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
β-N-Acetylhexosaminidases (HexNAcases) are versatile biocatalysts that cleave terminal N-acetylhexosamine units from various glycoconjugates. Established strategies to generate glycoside-forming versions of the wild type enzymes rely on the mutation of their catalytic residues; however, successful examples of synthetically useful HexNAcase mutants are scarce. In order to expand the range of HexNAcases available as targets for enzyme engineering, we functionally screened a metagenomic library derived from a human gut microbiome. From a pool of hits, we characterized four of the more active candidates by sequence analysis and phylogenetic mapping, and found that they all belonged to CAZy family GH20. After detailed kinetic analysis and characterization of their substrate specificities, active site mutants were generated which resulted in the identification of two new thioglycoligases. BvHex E294A and AsHex E301A catalyzed glycosyl transfer to all three of the 3-, 4- and 6-thio-N-acetylglucosaminides (thio-GlcNAcs) that were tested. Both mutant enzymes also catalyzed glycosyl transfer to a cysteine-containing variant of the model peptide Tab1, with AsHex E301A also transferring GlcNAc onto a thiol-containing protein. This work illustrates how large scale functional screening of expressed gene libraries allows the relatively rapid development of useful new glycoside-forming mutants of HexNAcases, expanding the pool of biocatalysts for carbohydrate synthesis.
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Affiliation(s)
- Gregor Tegl
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
| | - Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
| | - Katharina Ostmann
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
| | - John Hanson
- Department of Chemistry, University of Puget Sound, Tacoma, USA
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, Canada.
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89
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Adams AND, Azam MS, Costliow ZA, Ma X, Degnan PH, Vanderpool CK. A Novel Family of RNA-Binding Proteins Regulate Polysaccharide Metabolism in Bacteroides thetaiotaomicron. J Bacteriol 2021; 203:e0021721. [PMID: 34251866 PMCID: PMC8508124 DOI: 10.1128/jb.00217-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/08/2021] [Indexed: 11/20/2022] Open
Abstract
Human gut microbiome composition is constantly changing, and diet is a major driver of these changes. Gut microbial species that persist in mammalian hosts for long periods of time must possess mechanisms for sensing and adapting to nutrient shifts to avoid being outcompeted. Global regulatory mechanisms mediated by RNA-binding proteins (RBPs) that govern responses to nutrient shifts have been characterized in Proteobacteria and Firmicutes but remain undiscovered in the Bacteroidetes. Here, we report the identification of RBPs that are broadly distributed across the Bacteroidetes, with many genomes encoding multiple copies. Genes encoding these RBPs are highly expressed in many Bacteroides species. A purified RBP, RbpB, from Bacteroides thetaiotaomicron binds to single-stranded RNA in vitro with an affinity similar to other characterized regulatory RBPs. B. thetaiotaomicron mutants lacking RBPs show dramatic shifts in expression of polysaccharide utilization and capsular polysaccharide loci, suggesting that these RBPs may act as global regulators of polysaccharide metabolism. A B. thetaiotaomicron ΔrbpB mutant shows a growth defect on dietary sugars belonging to the raffinose family of oligosaccharides (RFOs). The ΔrbpB mutant had reduced expression of BT1871, encoding a predicted RFO-degrading melibiase, compared to the wild-type strain. Mutation of BT1871 confirmed that the enzyme it encodes is essential for growth on melibiose and promotes growth on the RFOs raffinose and stachyose. Our data reveal that RbpB is required for optimal expression of BT1871 and other polysaccharide-related genes, suggesting that we have identified an important new family of global regulatory proteins in the Bacteroidetes. IMPORTANCE The human colon houses hundreds of bacterial species, including many belonging to the genus Bacteroides, that aid in breaking down our food to keep us healthy. Bacteroides have many genes responsible for breaking down different dietary carbohydrates, and complex regulatory mechanisms ensure that specific genes are only expressed when the right carbohydrates are available. In this study, we discovered that Bacteroides use a family of RNA-binding proteins as global regulators to coordinate expression of carbohydrate utilization genes. The ability to turn different carbohydrate utilization genes on and off in response to changing nutrient conditions is critical for Bacteroides to live successfully in the gut, and thus the new regulators we have identified may be important for life in the host.
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Affiliation(s)
- Amanda N. D. Adams
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Muhammad S. Azam
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zachary A. Costliow
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Xiangqian Ma
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Patrick H. Degnan
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, California, USA
| | - Carin K. Vanderpool
- Department of Microbiology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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90
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Colnet B, Sieber CMK, Perraudeau F, Leclerc M. FiberGrowth Pipeline: A Framework Toward Predicting Fiber-Specific Growth From Human Gut Bacteroidetes Genomes. Front Microbiol 2021; 12:632567. [PMID: 34690938 PMCID: PMC8527192 DOI: 10.3389/fmicb.2021.632567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Dietary fibers impact gut colonic health, through the production of short-chain fatty acids. A low-fiber diet has been linked to lower bacterial diversity, obesity, type 2 diabetes, and promotion of mucosal pathogens. Glycoside hydrolases (GHs) are important enzymes involved in the bacterial catabolism of fiber into short-chain fatty acids. However, the GH involved in glycan breakdown (adhesion, hydrolysis, and fermentation) are organized in polysaccharide utilization loci (PUL) with complex modularity. Our goal was to explore how the capacity of strains, from the Bacteroidetes phylum, to grow on fiber could be predicted from their genome sequences. We designed an in silico pipeline called FiberGrowth and independently validated it for seven different fibers, on 28 genomes from Bacteroidetes-type strains. To do so, we compared the existing GH annotation tools and built PUL models by using published growth and gene expression data. FiberGrowth's prediction performance in terms of true positive rate (TPR) and false positive rate (FPR) strongly depended on available data and fiber: arabinoxylan (TPR: 0.89 and FPR: 0), inulin (0.95 and 0.33), heparin (0.8 and 0.22) laminarin (0.38 and 0.17), levan (0.3 and 0.06), mucus (0.13 and 0.38), and starch (0.73 and 0.41). Being able to better predict fiber breakdown by bacterial strains would help to understand their impact on human nutrition and health. Assuming further gene expression experiment along with discoveries on structural analysis, we hope computational tools like FiberGrowth will help researchers prioritize and design in vitro experiments.
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Affiliation(s)
- Bénédicte Colnet
- Pendulum Therapeutics, San Francisco, CA, United States
- Mines Paristech, Paris, France
| | | | | | - Marion Leclerc
- Université Paris Saclay, INRAe, AgroParisTech, Micalis Institute, Jouy en Josas, France
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91
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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: 99] [Impact Index Per Article: 33.0] [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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92
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Kmezik C, Krska D, Mazurkewich S, Larsbrink J. Characterization of a novel multidomain CE15-GH8 enzyme encoded by a polysaccharide utilization locus in the human gut bacterium Bacteroides eggerthii. Sci Rep 2021; 11:17662. [PMID: 34480044 PMCID: PMC8417218 DOI: 10.1038/s41598-021-96659-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/11/2021] [Indexed: 11/13/2022] Open
Abstract
Bacteroidetes are efficient degraders of complex carbohydrates, much thanks to their use of polysaccharide utilization loci (PULs). An integral part of PULs are highly specialized carbohydrate-active enzymes, sometimes composed of multiple linked domains with discrete functions—multicatalytic enzymes. We present the biochemical characterization of a multicatalytic enzyme from a large PUL encoded by the gut bacterium Bacteroides eggerthii. The enzyme, BeCE15A-Rex8A, has a rare and novel architecture, with an N-terminal carbohydrate esterase family 15 (CE15) domain and a C-terminal glycoside hydrolase family 8 (GH8) domain. The CE15 domain was identified as a glucuronoyl esterase (GE), though with relatively poor activity on GE model substrates, attributed to key amino acid substitutions in the active site compared to previously studied GEs. The GH8 domain was shown to be a reducing-end xylose-releasing exo-oligoxylanase (Rex), based on having activity on xylooligosaccharides but not on longer xylan chains. The full-length BeCE15A-Rex8A enzyme and the Rex domain were capable of boosting the activity of a commercially available GH11 xylanase on corn cob biomass. Our research adds to the understanding of multicatalytic enzyme architectures and showcases the potential of discovering novel and atypical carbohydrate-active enzymes from mining PULs.
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Affiliation(s)
- Cathleen Kmezik
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Daniel Krska
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Scott Mazurkewich
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden.,Wallenberg Wood Science Center, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Johan Larsbrink
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden. .,Wallenberg Wood Science Center, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
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93
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Abstract
The human gut microbiota (HGM) contributes to the physiology and health of its host. The health benefits provided by dietary manipulation of the HGM require knowledge of how glycans, the major nutrients available to this ecosystem, are metabolized. Arabinogalactan proteins (AGPs) are a ubiquitous feature of plant polysaccharides available to the HGM. Although the galactan backbone and galactooligosaccharide side chains of AGPs are conserved, the decorations of these structures are highly variable. Here, we tested the hypothesis that these variations in arabinogalactan decoration provide a selection mechanism for specific Bacteroides species within the HGM. The data showed that only a single bacterium, B. plebeius, grew on red wine AGP (Wi-AGP) and seaweed AGP (SW-AGP) in mono- or mixed culture. Wi-AGP thus acts as a privileged nutrient for a Bacteroides species within the HGM that utilizes marine and terrestrial plant glycans. The B. plebeius polysaccharide utilization loci (PULs) upregulated by AGPs encoded a polysaccharide lyase, located in the enzyme family GH145, which hydrolyzed Rha-Glc linkages in Wi-AGP. Further analysis of GH145 identified an enzyme with two active sites that displayed glycoside hydrolase and lyase activities, respectively, which conferred substrate flexibility for different AGPs. The AGP-degrading apparatus of B. plebeius also contained a sulfatase, BpS1_8, active on SW-AGP and Wi-AGP, which played a pivotal role in the utilization of these glycans by the bacterium. BpS1_8 enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health. IMPORTANCE Dietary manipulation of the HGM requires knowledge of how glycans available to this ecosystem are metabolized. The variable structures that decorate the core component of plant AGPs may influence their utilization by specific organisms within the HGM. Here, we evaluated the ability of Bacteroides species to utilize a marine and terrestrial AGP. The data showed that a single bacterium, B. plebeius, grew on Wi-AGP and SW-AGP in mono- or mixed culture. Wi-AGP is thus a privileged nutrient for a Bacteroides species that utilizes marine and terrestrial plant glycans. A key component of the AGP-degrading apparatus of B. plebeius is a sulfatase that conferred the ability of the bacterium to utilize these glycans. The enzyme enabled other Bacteroides species to access the sulfated AGPs, providing a route to introducing privileged nutrient utilization into probiotic and commensal organisms that could improve human health.
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94
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Gao G, Cao J, Mi L, Feng D, Deng Q, Sun X, Zhang H, Wang Q, Wang J. BdPUL12 depolymerizes β-mannan-like glycans into mannooligosaccharides and mannose, which serve as carbon sources for Bacteroides dorei and gut probiotics. Int J Biol Macromol 2021; 187:664-674. [PMID: 34339781 DOI: 10.1016/j.ijbiomac.2021.07.172] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 12/16/2022]
Abstract
Symbiotic bacteria, including members of the Bacteroides genus, are known to digest dietary fibers in the gastrointestinal tract. The metabolism of complex carbohydrates is restricted to a specified subset of species and is likely orchestrated by polysaccharide utilization loci (PULs) in these microorganisms. β-Mannans are plant cell wall polysaccharides that are commonly found in human nutrients. Here, we report the structural basis of a PUL cluster, BdPUL12, which controls β-mannan-like glycan catabolism in Bacteroides dorei. Detailed biochemical characterization and targeted gene disruption studies demonstrated that a key glycoside hydrolase, BdP12GH26, performs the initial attack on galactomannan or glucomannan likely via an endo-acting mode, generating mannooligosaccharides and mannose. Importantly, coculture assays showed that the B. dorei promoted the proliferation of Lactobacillus helveticus and Bifidobacterium adolescentis, likely by sharing mannooligosaccharides and mannose with these gut probiotics. Our findings provide new insights into carbohydrate metabolism in gut-inhabiting bacteria and lay a foundation for novel probiotic development.
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Affiliation(s)
- Ge Gao
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiawen Cao
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lan Mi
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Dan Feng
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qian Deng
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaobao Sun
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huien Zhang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China
| | - Qian Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jiakun Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China.
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95
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Sun HZ, Peng KL, Xue MY, Liu JX. Metagenomics analysis revealed the distinctive ruminal microbiome and resistive profiles in dairy buffaloes. Anim Microbiome 2021; 3:44. [PMID: 34210366 PMCID: PMC8247143 DOI: 10.1186/s42523-021-00103-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 05/31/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Antimicrobial resistance poses super challenges in both human health and livestock production. Rumen microbiota is a large reservoir of antibiotic resistance genes (ARGs), which show significant varations in different host species and lifestyles. To compare the microbiome and resistome between dairy cows and dairy buffaloes, the microbial composition, functions and harbored ARGs of rumen microbiota were explored between 16 dairy cows (3.93 ± 1.34 years old) and 15 dairy buffaloes (4.80 ± 3.49 years old) using metagenomics. RESULTS Dairy buffaloes showed significantly different bacterial species (LDA > 3.5 & P < 0.01), enriched KEGG pathways and CAZymes encoded genes (FDR < 0.01 & Fold Change > 2) in the rumen compared with dairy cows. Distinct resistive profiles were identified between dairy cows and dairy buffaloes. Among the total 505 ARGs discovered in the resistome of dairy cows and dairy buffaloes, 18 ARGs conferring resistance to 16 antibiotic classes were uniquely detected in dairy buffaloes. Gene tcmA (resistance to tetracenomycin C) presented high prevalence and age effect in dairy buffaloes, and was also highly positively correlated with 93 co-expressed ARGs in the rumen (R = 0.98 & P = 5E-11). In addition, 44 bacterial species under Lactobacillus genus were found to be associated with tcmA (R > 0.95 & P < 0.001). L. amylovorus and L. acidophilus showed greatest potential of harboring tcmA based on co-occurrence analysis and tcmA-containing contigs taxonomic alignment. CONCLUSIONS The current study revealed distinctive microbiome and unique ARGs in dairy buffaloes compared to dairy cattle. Our results provide novel understanding on the microbiome and resistome of dairy buffaloes, the unique ARGs and associated bacteria will help develop strategies to prevent the transmission of ARGs.
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Affiliation(s)
- Hui-Zeng Sun
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ke-Lan Peng
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Ming-Yuan Xue
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Jian-Xin Liu
- Institute of Dairy Science, Ministry of Education Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou, 310058 China
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96
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Vieira PS, Bonfim IM, Araujo EA, Melo RR, Lima AR, Fessel MR, Paixão DAA, Persinoti GF, Rocco SA, Lima TB, Pirolla RAS, Morais MAB, Correa JBL, Zanphorlin LM, Diogo JA, Lima EA, Grandis A, Buckeridge MS, Gozzo FC, Benedetti CE, Polikarpov I, Giuseppe PO, Murakami MT. Xyloglucan processing machinery in Xanthomonas pathogens and its role in the transcriptional activation of virulence factors. Nat Commun 2021; 12:4049. [PMID: 34193873 PMCID: PMC8245568 DOI: 10.1038/s41467-021-24277-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023] Open
Abstract
Xyloglucans are highly substituted and recalcitrant polysaccharides found in the primary cell walls of vascular plants, acting as a barrier against pathogens. Here, we reveal that the diverse and economically relevant Xanthomonas bacteria are endowed with a xyloglucan depolymerization machinery that is linked to pathogenesis. Using the citrus canker pathogen as a model organism, we show that this system encompasses distinctive glycoside hydrolases, a modular xyloglucan acetylesterase and specific membrane transporters, demonstrating that plant-associated bacteria employ distinct molecular strategies from commensal gut bacteria to cope with xyloglucans. Notably, the sugars released by this system elicit the expression of several key virulence factors, including the type III secretion system, a membrane-embedded apparatus to deliver effector proteins into the host cells. Together, these findings shed light on the molecular mechanisms underpinning the intricate enzymatic machinery of Xanthomonas to depolymerize xyloglucans and uncover a role for this system in signaling pathways driving pathogenesis.
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Affiliation(s)
- Plinio S. Vieira
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Isabela M. Bonfim
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, São Paulo Brazil
| | - Evandro A. Araujo
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil ,grid.452567.70000 0004 0445 0877Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Ricardo R. Melo
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Augusto R. Lima
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Melissa R. Fessel
- grid.418514.d0000 0001 1702 8585Butantan Institute, Butantan Foundation, São Paulo, São Paulo Brazil
| | - Douglas A. A. Paixão
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Gabriela F. Persinoti
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Silvana A. Rocco
- grid.452567.70000 0004 0445 0877Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Tatiani B. Lima
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Renan A. S. Pirolla
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Mariana A. B. Morais
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Jessica B. L. Correa
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Leticia M. Zanphorlin
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Jose A. Diogo
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil ,grid.411087.b0000 0001 0723 2494Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, São Paulo Brazil
| | - Evandro A. Lima
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Adriana Grandis
- grid.11899.380000 0004 1937 0722Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Marcos S. Buckeridge
- grid.11899.380000 0004 1937 0722Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Fabio C. Gozzo
- grid.411087.b0000 0001 0723 2494Institute of Chemistry, University of Campinas, Campinas, São Paulo Brazil
| | - Celso E. Benedetti
- grid.452567.70000 0004 0445 0877Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Igor Polikarpov
- grid.11899.380000 0004 1937 0722São Carlos Institute of Physics, University of São Paulo, São Carlos, São Paulo Brazil
| | - Priscila O. Giuseppe
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
| | - Mario T. Murakami
- grid.452567.70000 0004 0445 0877Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo Brazil
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97
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Yang X, Yang X, Yu H, Na L, Ghosh T, McArthur JB, Chou TF, Dickson P, Chen X. A GH89 human α-N-acetylglucosaminidase (hNAGLU) homologue from gut microbe Bacteroides thetaiotaomicron capable of hydrolyzing heparosan oligosaccharides. AMB Express 2021; 11:94. [PMID: 34165649 PMCID: PMC8225759 DOI: 10.1186/s13568-021-01253-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
Carbohydrate-Active enZYme (CAZY) GH89 family enzymes catalyze the cleavage of terminal α-N-acetylglucosamine from glycans and glycoconjugates. Although structurally and mechanistically similar to the human lysosomal α-N-acetylglucosaminidase (hNAGLU) in GH89 which is involved in the degradation of heparan sulfate in the lysosome, the reported bacterial GH89 enzymes characterized so far have no or low activity toward α-N-acetylglucosamine-terminated heparosan oligosaccharides, the preferred substrates of hNAGLU. We cloned and expressed several soluble and active recombinant bacterial GH89 enzymes in Escherichia coli. Among these enzymes, a truncated recombinant α-N-acetylglucosaminidase from gut symbiotic bacterium Bacteroides thetaiotaomicron ∆22Bt3590 was found to catalyze the cleavage of the terminal α1-4-linked N-acetylglucosamine (GlcNAc) from a heparosan disaccharide with high efficiency. Heparosan oligosaccharides with lengths up to decasaccharide were also suitable substrates. This bacterial α-N-acetylglucosaminidase could be a useful catalyst for heparan sulfate analysis.
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Affiliation(s)
- Xiaohong Yang
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Xiaoxiao Yang
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Lan Na
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Rosalind Franklin Institute and University of Oxford, Harwell Campus, Didcot, OX11 0FA, UK
| | - Tamashree Ghosh
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - John B McArthur
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA
- Integrated Micro-Chromatography Systems, Inc, Irmo, SC, 20963, USA
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Xi Chen
- Department of Chemistry, University of California, One Shields Avenue, Davis, CA, 95616, USA.
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98
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Hameleers L, Penttinen L, Ikonen M, Jaillot L, Fauré R, Terrapon N, Deuss PJ, Hakulinen N, Master ER, Jurak E. Polysaccharide utilization loci-driven enzyme discovery reveals BD-FAE: a bifunctional feruloyl and acetyl xylan esterase active on complex natural xylans. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:127. [PMID: 34059129 PMCID: PMC8165983 DOI: 10.1186/s13068-021-01976-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/19/2021] [Indexed: 05/10/2023]
Abstract
BACKGROUND Nowadays there is a strong trend towards a circular economy using lignocellulosic biowaste for the production of biofuels and other bio-based products. The use of enzymes at several stages of the production process (e.g., saccharification) can offer a sustainable route due to avoidance of harsh chemicals and high temperatures. For novel enzyme discovery, physically linked gene clusters targeting carbohydrate degradation in bacteria, polysaccharide utilization loci (PULs), are recognized 'treasure troves' in the era of exponentially growing numbers of sequenced genomes. RESULTS We determined the biochemical properties and structure of a protein of unknown function (PUF) encoded within PULs of metagenomes from beaver droppings and moose rumen enriched on poplar hydrolysate. The corresponding novel bifunctional carbohydrate esterase (CE), now named BD-FAE, displayed feruloyl esterase (FAE) and acetyl esterase activity on simple, synthetic substrates. Whereas acetyl xylan esterase (AcXE) activity was detected on acetylated glucuronoxylan from birchwood, only FAE activity was observed on acetylated and feruloylated xylooligosaccharides from corn fiber. The genomic contexts of 200 homologs of BD-FAE revealed that the 33 closest homologs appear in PULs likely involved in xylan breakdown, while the more distant homologs were found either in alginate-targeting PULs or else outside PUL contexts. Although the BD-FAE structure adopts a typical α/β-hydrolase fold with a catalytic triad (Ser-Asp-His), it is distinct from other biochemically characterized CEs. CONCLUSIONS The bifunctional CE, BD-FAE, represents a new candidate for biomass processing given its capacity to remove ferulic acid and acetic acid from natural corn and birchwood xylan substrates, respectively. Its detailed biochemical characterization and solved crystal structure add to the toolbox of enzymes for biomass valorization as well as structural information to inform the classification of new CEs.
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Affiliation(s)
- Lisanne Hameleers
- Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Leena Penttinen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Martina Ikonen
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
| | - Léa Jaillot
- Architecture Et Fonction Des Macromolécules Biologiques (AFMB), UMR7257 Centre National de La Recherche Scientifique (CNRS) and Aix-Marseille Université (AMU), USC1408 Institut National de Recherche Pour L'Agriculture, l'Alimentation Et L'Environnement (INRAE), 13288, Marseille cedex 9, France
| | - Régis Fauré
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Nicolas Terrapon
- Architecture Et Fonction Des Macromolécules Biologiques (AFMB), UMR7257 Centre National de La Recherche Scientifique (CNRS) and Aix-Marseille Université (AMU), USC1408 Institut National de Recherche Pour L'Agriculture, l'Alimentation Et L'Environnement (INRAE), 13288, Marseille cedex 9, France
| | - Peter J Deuss
- Department of Chemical Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Nina Hakulinen
- Department of Chemistry, University of Eastern Finland, Yliopistokatu 7, 80130, Joensuu, Finland
| | - Emma R Master
- Department of Bioproducts and Biosystems, Aalto University, Kemistintie 1, 02150, Espoo, Finland
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
| | - Edita Jurak
- Department of Bioproduct Engineering, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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99
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A Novel Auxiliary Agarolytic Pathway Expands Metabolic Versatility in the Agar-Degrading Marine Bacterium Colwellia echini A3 T. Appl Environ Microbiol 2021; 87:e0023021. [PMID: 33811026 DOI: 10.1128/aem.00230-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Marine microorganisms encode a complex repertoire of carbohydrate-active enzymes (CAZymes) for the catabolism of algal cell wall polysaccharides. While the core enzyme cascade for degrading agar is conserved across agarolytic marine bacteria, gain of novel metabolic functions can lead to the evolutionary expansion of the gene repertoire. Here, we describe how two less-abundant GH96 α-agarases harbored in the agar-specific polysaccharide utilization locus (PUL) of Colwellia echini strain A3T facilitate the versatility of the agarolytic pathway. The cellular and molecular functions of the α-agarases examined by genomic, transcriptomic, and biochemical analyses revealed that α-agarases of C. echini A3T create a novel auxiliary pathway. α-Agarases convert even-numbered neoagarooligosaccharides to odd-numbered agaro- and neoagarooligosaccharides, providing an alternative route for the depolymerization process in the agarolytic pathway. Comparative genomic analysis of agarolytic bacteria implied that the agarolytic gene repertoire in marine bacteria has been diversified during evolution, while the essential core agarolytic gene set has been conserved. The expansion of the agarolytic gene repertoire and novel hydrolytic functions, including the elucidated molecular functionality of α-agarase, promote metabolic versatility by channeling agar metabolism through different routes. IMPORTANCE Colwellia echini A3T is an example of how the gain of gene(s) can lead to the evolutionary expansion of agar-specific polysaccharide utilization loci (PUL). C. echini A3T encodes two α-agarases in addition to the core β-agarolytic enzymes in its agarolytic PUL. Among the agar-degrading CAZymes identified so far, only a few α-agarases have been biochemically characterized. The molecular and biological functions of two α-agarases revealed that their unique hydrolytic pattern leads to the emergence of auxiliary agarolytic pathways. Through the combination of transcriptomic, genomic, and biochemical evidence, we elucidate the complete α-agarolytic pathway in C. echini A3T. The addition of α-agarases to the agarolytic enzyme repertoire might allow marine agarolytic bacteria to increase competitive abilities through metabolic versatility.
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Genome Features of Asaia sp. W12 Isolated from the Mosquito Anopheles stephensi Reveal Symbiotic Traits. Genes (Basel) 2021; 12:genes12050752. [PMID: 34067621 PMCID: PMC8156966 DOI: 10.3390/genes12050752] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/29/2023] Open
Abstract
Asaia bacteria commonly comprise part of the microbiome of many mosquito species in the genera Anopheles and Aedes, including important vectors of infectious agents. Their close association with multiple organs and tissues of their mosquito hosts enhances the potential for paratransgenesis for the delivery of antimalaria or antivirus effectors. The molecular mechanisms involved in the interactions between Asaia and mosquito hosts, as well as Asaia and other bacterial members of the mosquito microbiome, remain underexplored. Here, we determined the genome sequence of Asaia strain W12 isolated from Anopheles stephensi mosquitoes, compared it to other Asaia species associated with plants or insects, and investigated the properties of the bacteria relevant to their symbiosis with mosquitoes. The assembled genome of strain W12 had a size of 3.94 MB, the largest among Asaia spp. studied so far. At least 3585 coding sequences were predicted. Insect-associated Asaia carried more glycoside hydrolase (GH)-encoding genes than those isolated from plants, showing their high plant biomass-degrading capacity in the insect gut. W12 had the most predicted regulatory protein components comparatively among the selected Asaia, indicating its capacity to adapt to frequent environmental changes in the mosquito gut. Two complete operons encoding cytochrome bo3-type ubiquinol terminal oxidases (cyoABCD-1 and cyoABCD-2) were found in most Asaia genomes, possibly offering alternative terminal oxidases and allowing the flexible transition of respiratory pathways. Genes involved in the production of 2,3-butandiol and inositol have been found in Asaia sp. W12, possibly contributing to biofilm formation and stress tolerance.
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