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Wardman JF, Withers SG. Carbohydrate-active enzyme (CAZyme) discovery and engineering via (Ultra)high-throughput screening. RSC Chem Biol 2024; 5:595-616. [PMID: 38966674 PMCID: PMC11221537 DOI: 10.1039/d4cb00024b] [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: 01/23/2024] [Accepted: 05/16/2024] [Indexed: 07/06/2024] Open
Abstract
Carbohydrate-active enzymes (CAZymes) constitute a diverse set of enzymes that catalyze the assembly, degradation, and modification of carbohydrates. These enzymes have been fashioned into potent, selective catalysts by millennia of evolution, and yet are also highly adaptable and readily evolved in the laboratory. To identify and engineer CAZymes for different purposes, (ultra)high-throughput screening campaigns have been frequently utilized with great success. This review provides an overview of the different approaches taken in screening for CAZymes and how mechanistic understandings of CAZymes can enable new approaches to screening. Within, we also cover how cutting-edge techniques such as microfluidics, advances in computational approaches and synthetic biology, as well as novel assay designs are leading the field towards more informative and effective screening approaches.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia Vancouver BC V6T 1Z3 Canada
- Michael Smith Laboratories, University of British Columbia Vancouver BC V6T 1Z4 Canada
- Department of Chemistry, University of British Columbia Vancouver BC V6T 1Z1 Canada
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2
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Li W, Wang L, Li X, Zheng X, Cohen MF, Liu YX. Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functional CopA in Environmental Microbiomes. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:1182-1194. [PMID: 36089219 PMCID: PMC11082258 DOI: 10.1016/j.gpb.2022.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 06/15/2023]
Abstract
Exploring the natural diversity of functional genes/proteins from environmental DNA in high throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper (Cu) resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins were distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.
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Affiliation(s)
- Wenjun Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Likun Wang
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Xiaofang Li
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China.
| | - Xin Zheng
- Hebei Key Laboratory of Soil Ecology, Centre for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China
| | - Michael F Cohen
- Department of Biology, Sonoma State University, Rohnert Park, CA 94928, USA
| | - Yong-Xin Liu
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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3
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Xue Y, Zheng M, Wu S, Liu Y, Huang X. Changes in the Species and Functional Composition of Activated Sludge Communities Revealed Mechanisms of Partial Nitrification Established by Ultrasonication. Front Microbiol 2022; 13:960608. [PMID: 35928152 PMCID: PMC9344063 DOI: 10.3389/fmicb.2022.960608] [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: 06/03/2022] [Accepted: 06/22/2022] [Indexed: 11/20/2022] Open
Abstract
To achieve energy-efficient shortcut nitrogen removal of wastewater in the future, selective elimination of nitrite-oxidizing bacteria (NOB) while enriching ammonia-oxidizing microorganisms is a crucial step. However, the underlying mechanisms of partial nitrification are still not well understood, especially the newly discovered ultrasound-based partial nitrification. To elucidate this issue, in this study two bioreactors were set up, with one established partial nitrification by ultrasonication while the other didn't. During the operation of both reactors, the taxonomic and functional composition of the microbial community were investigated through metagenomics analysis. The result showed that during ultrasonic partial nitrification, ammonia-oxidizing archaea (AOA), Nitrososphaerales, was enriched more than ammonia-oxidizing bacteria (AOB), Nitrosomonas. The enrichment of microorganisms in the community increased the abundance of genes involved in microbial energy generation from lipid and carbohydrates. On the other hand, the abundance of NOB, Nitrospira and Nitrolancea, and Comammox Nitrospira decreased. Selective inhibition of NOB was highly correlated with genes involved in signal transduction enzymes, such as encoding histidine kinase and serine/threonine kinase. These findings provided deep insight into partial nitrification and contributed to the development of shortcut nitrification in wastewater treatment plants.
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Affiliation(s)
- Yu Xue
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, QLD, Australia
| | - Shuang Wu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Yanchen Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
- *Correspondence: Yanchen Liu
| | - Xia Huang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
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4
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Wu Z, Zhang Y, Nie G, Liu J, Mei H, He Z, Dou P, Wang K. Tracking the gastrointestinal digestive and metabolic behaviour of Dendrobium officinale polysaccharides by fluorescent labelling. Food Funct 2022; 13:7274-7286. [PMID: 35726749 DOI: 10.1039/d2fo01506d] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recently, Dendrobium officinale polysaccharide (DOP), a typical acetylated glucomannan, has been widely applied in functional foods owing to its excellent bioactivity. However, the insufficiency of studies on in vivo process severely limits the further utilization of DOP. The aim of this study was to systematically investigate the gastrointestinal digestive behaviour of DOP after oral administration by labelling it with two fluorescein aminopyrene-1,3,6-trisulfonic acids, trisodium salt (APTS) and cyanine 7.5 (Cy7.5). Combining the results of NIR imaging and HPGPC, we found that DOP was poorly absorbed directly in the prototype form; instead, DOP moved with the intestinal contents to the distal part of the intestine, where Bacteroides aggregated for a prolonged time and was metabolized to oligosaccharide-like substances. In contrast, the digestive degradation of DOP in pseudo-sterile mice with a targeted clearance of Bacteroides significantly weakened, which provided the basis and direction for the subsequent search for more specific metabolic pathways of DOP in vivo.
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Affiliation(s)
- Zhijing Wu
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China.,Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, 430030 Wuhan, PR China
| | - Yu Zhang
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China.,Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, 430030 Wuhan, PR China
| | - Gang Nie
- Hubei Key Laboratory of Nature Medicinal Chemistry and Resource Evaluation, Tongji Medical College of Pharmacy, Huazhong University of Science and Technology, 430030 Wuhan, China.
| | - Junxi Liu
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China.,Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, 430030 Wuhan, PR China
| | - Hao Mei
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China.,Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, 430030 Wuhan, PR China
| | - Zihao He
- Department of Pharmacy, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, China.,Hubei Province Clinical Research Center for Precision Medicine for Critical Illness, 430030 Wuhan, PR China
| | - Pengfei Dou
- Hubei Key Laboratory of Nature Medicinal Chemistry and Resource Evaluation, Tongji Medical College of Pharmacy, Huazhong University of Science and Technology, 430030 Wuhan, China.
| | - Kaiping Wang
- Hubei Key Laboratory of Nature Medicinal Chemistry and Resource Evaluation, Tongji Medical College of Pharmacy, Huazhong University of Science and Technology, 430030 Wuhan, China.
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5
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Liu F, Chen HM, Armstrong Z, Withers SG. Azido Groups Hamper Glycan Acceptance by Carbohydrate Processing Enzymes. ACS CENTRAL SCIENCE 2022; 8:656-662. [PMID: 35647280 PMCID: PMC9136970 DOI: 10.1021/acscentsci.1c01172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Indexed: 06/15/2023]
Abstract
Azido sugars have found frequent use as probes of biological systems in approaches ranging from cell surface metabolic labeling to activity-based proteomic profiling of glycosidases. However, little attention is typically paid to how well azide-substituted sugars represent the parent molecule, despite the substantial difference in size and structure of an azide compared to a hydroxyl. To quantitatively assess how well azides are accommodated, we have used glycosidases as tractable model enzyme systems reflecting what would also be expected for glycosyltransferases and other sugar binding/modifying proteins. In this vein, specificity constants have been measured for the hydrolysis of a series of azidodeoxy glucosides and N-acetylhexosaminides by a large number of glycosidases produced from expressed synthetic gene and metagenomic libraries. Azides at secondary carbons are not significantly accommodated, and thus, associated substrates are not processed, while those at primary carbons are productively recognized by only a small subset of the enzymes and often then only very poorly. Accordingly, in the absence of careful controls, results obtained with azide-modified sugars may not be representative of the situation with the natural sugar and should be interpreted with considerable caution. Azide incorporation can indeed provide a useful tool to monitor and detect glycosylation, but careful consideration should go into the selection of sites of azide substitution; such studies should not be used to quantitate glycosylation or to infer the absence of glycosylation activity.
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6
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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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7
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Zeng Y, Pu Y, Niu L, Deng J, Zeng D, Amato K, Li Y, Zhou Y, Lin Y, Wang J, Wu L, Chen B, Pan K, Jing B, Ni X. Comparison of gastrointestinal microbiota in golden snub-nosed monkey (Rhinopithecus roxellanae), green monkey (Chlorocebus aethiops sabaeus), and ring-tailed lemur (Lemur catta) by high throughput sequencing. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2021.e01946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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8
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Differences in Fecal Microbiome and Antimicrobial Resistance between Captive and Free-Range Sika Deer under the Same Exposure of Antibiotic Anthelmintics. Microbiol Spectr 2021; 9:e0191821. [PMID: 34851181 PMCID: PMC8635127 DOI: 10.1128/spectrum.01918-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
This study aimed to compare the fecal microbiome and antimicrobial resistance between captive and free-range sika deer with the same exposure to antibiotic anthelmintics. The taxonomic differences mainly involved significant changes in the dominant phyla, genera, and species. Linear discriminant analysis effect size (LEfSe) analysis revealed that 22 taxa were significantly different between the two groups. The KEGG analysis showed that the fecal microbiome metabolic function, and all level 2 categories in metabolism had higher abundance in the free-range deer. Based on the carbohydrate-active enzyme (CAZy) database analysis, glycoside hydrolases and carbohydrate-binding modules showed remarkable differences between the two groups. Regarding antibiotic resistance, tetQ and lnuC dominated the antibiotic resistance ontology (ARO) terms, and tetracycline and lincosamide resistance dominated the antimicrobial resistance patterns. Furthermore, the lnuC, ErmF, and tetW/N/W AROs and lincosamide resistance showed higher abundance in the captive deer, suggesting that captivity may yield more serious resistance issues because of the differences in greenfeed diet, breeding density, and/or housing environment. The results also revealed important associations between the phylum Proteobacteria, genus Prevotella, and major antibiotic resistance genes. Although the present study was a pilot study with a limited sample size that was insufficient control for some potential factors, it serves as the metagenomic study on the microbial communities and antimicrobial resistance in sika deer. IMPORTANCE We used a metagenomic approach to investigate whether and how captive and free-range impact the microbial communities and antimicrobial resistance in sika deer. The results provide solid evidence of the significant impacts on the microbial composition and function in captive and free-range sika deer. Interestingly, although the sika deer had the same exposure to antibiotic anthelmintics, the antimicrobial resistances were affected by the breeding environment.
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9
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Chuckran PF, Hungate BA, Schwartz E, Dijkstra P. Variation in genomic traits of microbial communities among ecosystems. FEMS MICROBES 2021. [DOI: 10.1093/femsmc/xtab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
ABSTRACT
Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size—reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments—a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.
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Affiliation(s)
- Peter F Chuckran
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Bruce A Hungate
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Egbert Schwartz
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
| | - Paul Dijkstra
- Center for Ecosystem Science and Society (ECOSS) and Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, United States of America
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10
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Lopes EM, Passini MRZ, Kishi LT, Chen T, Paster BJ, Gomes BPFA. Interrelationship between the Microbial Communities of the Root Canals and Periodontal Pockets in Combined Endodontic-Periodontal Diseases. Microorganisms 2021; 9:microorganisms9091925. [PMID: 34576820 PMCID: PMC8465609 DOI: 10.3390/microorganisms9091925] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 12/31/2022] Open
Abstract
Periodontal and Endodontic diseases are biofilm-related diseases. The presence of microorganisms in root canals (RCs) and the complex microbiota of periodontal pockets (PPs) contribute to the development of endodontic-periodontal diseases. This study performed a systemic analysis using state-of-the-art sequence data to assess the microbial composition of infected RCs and PPs to further assess the microbiota and verify the possibility of cross-infection between these sites. The microbiomes of these combined diseases were examined with a focus on the V3-V4 hypervariable region of the 16S rRNA gene. The number of species in PP was higher than in RC, and there was a predominance of obligate anaerobes and gram-negative bacteria. In the RCs, the genera Enterococcus, Parvimonas, Stomatobaculum predominated, in contrast, the PPs revealed a predominance of Enterococcus, Parvimonas, Stomatobaculum, Peptostreptococcus and Mogibacterium. The RC and PP microbiome was not similar with regards to the sharing of OTUs for phyla and genera (8 and 67, respectively). The evaluation of molecular markers revealed a large number of markers for resistance to antibiotics of the carbapenem and beta-lactam type (broad spectrum). Another relevant finding of this study was the markers related to systemic diseases related to cardiac muscle and rheumatology, among others. In conclusion, the RC microbiota was less complex and diverse than PP. Interactions between microbial communities were present. The shared genus can signal communication between the endodontic and periodontal microbiomes.
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Affiliation(s)
- Erica M. Lopes
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas -UNICAMP, Piracicaba 13400-001, SP, Brazil;
- Correspondence: (E.M.L.); (B.P.F.A.G.)
| | - Maicon R. Z. Passini
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas -UNICAMP, Piracicaba 13400-001, SP, Brazil;
| | - Luciano T. Kishi
- National Laboratory of Scientific Computing, Petrópolis 25715-183, RJ, Brazil;
| | - Tsute Chen
- Department of Molecular Genetics, The Forsyth Institute, Cambridge, MA 02142, USA;
| | - Bruce J. Paster
- Microbiology Department, The Forsyth Institute, Cambridge, MA 02142, USA;
| | - Brenda P. F. A. Gomes
- Department of Restorative Dentistry, Division of Endodontics, Piracicaba Dental School, State University of Campinas -UNICAMP, Piracicaba 13400-001, SP, Brazil;
- Correspondence: (E.M.L.); (B.P.F.A.G.)
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11
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Tingley JP, Low KE, Xing X, Abbott DW. Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:16. [PMID: 33422151 PMCID: PMC7797155 DOI: 10.1186/s13068-020-01869-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/24/2020] [Indexed: 05/08/2023]
Abstract
The production of biofuels as an efficient source of renewable energy has received considerable attention due to increasing energy demands and regulatory incentives to reduce greenhouse gas emissions. Second-generation biofuel feedstocks, including agricultural crop residues generated on-farm during annual harvests, are abundant, inexpensive, and sustainable. Unlike first-generation feedstocks, which are enriched in easily fermentable carbohydrates, crop residue cell walls are highly resistant to saccharification, fermentation, and valorization. Crop residues contain recalcitrant polysaccharides, including cellulose, hemicelluloses, pectins, and lignin and lignin-carbohydrate complexes. In addition, their cell walls can vary in linkage structure and monosaccharide composition between plant sources. Characterization of total cell wall structure, including high-resolution analyses of saccharide composition, linkage, and complex structures using chromatography-based methods, nuclear magnetic resonance, -omics, and antibody glycome profiling, provides critical insight into the fine chemistry of feedstock cell walls. Furthermore, improving both the catalytic potential of microbial communities that populate biodigester reactors and the efficiency of pre-treatments used in bioethanol production may improve bioconversion rates and yields. Toward this end, knowledge and characterization of carbohydrate-active enzymes (CAZymes) involved in dynamic biomass deconstruction is pivotal. Here we overview the use of common "-omics"-based methods for the study of lignocellulose-metabolizing communities and microorganisms, as well as methods for annotation and discovery of CAZymes, and accurate prediction of CAZyme function. Emerging approaches for analysis of large datasets, including metagenome-assembled genomes, are also discussed. Using complementary glycomic and meta-omic methods to characterize agricultural residues and the microbial communities that digest them provides promising streams of research to maximize value and energy extraction from crop waste streams.
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Affiliation(s)
- Jeffrey P Tingley
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
- Department of Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 6T5, Canada
| | - Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403-1st Avenue South, Lethbridge, AB, T1J 4B1, Canada.
- Department of Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 6T5, Canada.
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12
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Yang S, Xie X, Ma J, He X, Li Y, Du M, Li L, Yang L, Wu Q, Chen W, Zhang J. Selective Isolation of Bifidobacterium From Human Faeces Using Pangenomics, Metagenomics, and Enzymology. Front Microbiol 2021; 12:649698. [PMID: 33967985 PMCID: PMC8096985 DOI: 10.3389/fmicb.2021.649698] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Bifidobacterium, an important genus for human health, is difficult to isolate. We applied metagenomics, pangenomics, and enzymology to determine the dominant glycoside hydrolase (GH) families of Bifidobacterium and designed selective medium for Bifidobacterium isolation. Pangenomics results showed that the GH13, GH3, GH42, and GH43 families were highly conserved in Bifidobacterium. Metagenomic analysis of GH families in human faecal samples was performed. The results indicated that Bifidobacterium contains core GHs for utilizing raffinose, D-trehalose anhydrous, D(+)-cellobiose, melibiose, lactulose, lactose, D(+)-sucrose, resistant starch, pullulan, xylan, and glucan. These carbohydrates as the main carbon sources were applied for selective media, which were more conducive to the growth of bifidobacteria. In the medium with lactose, raffinose and xylan as the main carbon sources, the ratio of cultivable bifidobacteria to cultivable microorganisms were 89.39% ± 2.50%, 71.45% ± 0.99%, and 53.95% ± 1.22%, respectively, whereas the ratio in the ordinary Gifu anaerobic medium was only 17.90% ± 0.58%. Furthermore, the species significantly (p < 0.05) varied among samples from different individuals. Results suggested that xylan might be a prebiotic that benefits host health, and it is feasible to screen and isolate bifidobacteria using the oligosaccharides corresponding to the specific GHs of bifidobacteria as the carbon sources of the selective media.
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Affiliation(s)
- Shuanghong Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xinqiang Xie
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Jun Ma
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xingxiang He
- Department of Gastroenterology, First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Ying Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Mingzhu Du
- School of Food Science and Technology, Jiangnan University, Wuxi, China
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Longyan Li
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Lingshuang Yang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
| | - Wei Chen
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Jumei Zhang
- Guangdong Provincial Key Laboratory of Microbial Safety and Health, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China
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13
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High-Throughput Generation of Product Profiles for Arabinoxylan-Active Enzymes from Metagenomes. Appl Environ Microbiol 2020; 86:AEM.01505-20. [PMID: 32948521 DOI: 10.1128/aem.01505-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/15/2020] [Indexed: 11/20/2022] Open
Abstract
Metagenomics is an exciting alternative to seek carbohydrate-active enzymes from a range of sources. Typically, metagenomics reveals dozens of putative catalysts that require functional characterization for further application in industrial processes. High-throughput screening methods compatible with adequate natural substrates are crucial for an accurate functional elucidation of substrate preferences. Based on DNA sequencer-aided fluorophore-assisted carbohydrate electrophoresis (DSA-FACE) analysis of enzymatic-reaction products, we generated product profiles to consequently infer substrate cleavage positions, resulting in the generation of enzymatic-degradation maps. Product profiles were produced in high throughput for arabinoxylan (AX)-active enzymes belonging to the glycoside hydrolase families GH43 (subfamilies 2 [MG432], 7 [MG437], and 28 [MG4328]) and GH8 (MG8) starting from 12 (arabino)xylo-oligosaccharides. These enzymes were discovered through functional metagenomic studies of feces from the North American beaver (Castor canadensis). This work shows how enzyme loading alters the product profiles of all enzymes studied and gives insight into AX degradation patterns, revealing sequential substrate preferences of AX-active enzymes.IMPORTANCE Arabinoxylan is mainly found in the hemicellulosic fractions of rice straw, corn cobs, and rice husk. Converting arabinoxylan into (arabino)xylo-oligosaccharides as added-value products that can be applied in food, feed, and cosmetics presents a sustainable and economic alternative for the biorefinery industries. Efficient and profitable AX degradation requires a set of enzymes with particular characteristics. Therefore, enzyme discovery and the study of substrate preferences are of utmost importance. Beavers, as consumers of woody biomass, are a promising source of a repertoire of enzymes able to deconstruct hemicelluloses into soluble oligosaccharides. High-throughput analysis of the oligosaccharide profiles produced by these enzymes will assist in the selection of the most appropriate enzymes for the biorefinery.
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14
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Ye M, Yu J, Shi X, Zhu J, Gao X, Liu W. Polysaccharides catabolism by the human gut bacterium - Bacteroides thetaiotaomicron: advances and perspectives. Crit Rev Food Sci Nutr 2020; 61:3569-3588. [PMID: 32779480 DOI: 10.1080/10408398.2020.1803198] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, the degradation processes of polysaccharides by human gut microbiota are receiving considerable attention due to the discoveries of the powerful function of gut microbiota. Gut microbiota has developed a sensitive, accurate, and complex system for sensing, capturing, and degrading different polysaccharides. Among the gut microbiota, Bacteroides thetaiotaomicron, a representative species of Bacteroides, is considered as the best degrader of polysaccharides and a potential probiotic in pharmaceutical and food industries. Here, we summarize the degradation system of B. thetaiotaomicron and the degradation pathways of different polysaccharides by B. thetaiotaomicron. We also describe a technical route for investigating a specific polysaccharide degradation pathway by human gut bacteria. In addition, we also provide the future perspectives in the development of novel polysaccharides or oligosaccharides drugs, precision microbiology medicine, and personalized nutrition.
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Affiliation(s)
- Meng Ye
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Juping Yu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Xuexia Shi
- Department of Clinical Pharmacy, Qinghai University Affiliated Hospital, Xining, PR China
| | - Jingyi Zhu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Xiangdong Gao
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China
| | - Wei Liu
- Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, State Key Laboratory of Natural Medicines, School of Life Science and Technology, China Pharmaceutical University, Nanjing, PR China.,Department of Clinical Pharmacy, Qinghai University Affiliated Hospital, Xining, PR China
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15
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Metagenomics-Guided Discovery of Potential Bacterial Metallothionein Genes from the Soil Microbiome That Confer Cu and/or Cd Resistance. Appl Environ Microbiol 2020; 86:AEM.02907-19. [PMID: 32111593 DOI: 10.1128/aem.02907-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/15/2020] [Indexed: 12/18/2022] Open
Abstract
Metallothionein (MT) genes are valuable genetic materials for developing metal bioremediation tools. Currently, a limited number of prokaryotic MTs have been experimentally identified, which necessitates the expansion of bacterial MT diversity. In this study, we conducted a metagenomics-guided analysis for the discovery of potential bacterial MT genes from the soil microbiome. More specifically, we combined resistance gene enrichment through diversity loss, metagenomic mining with a dedicated MT database, evolutionary trace analysis, DNA chemical synthesis, and functional genomic validation to identify novel MTs. Results showed that Cu stress induced a compositional change in the soil microbiome, with an enrichment of metal-resistant bacteria in soils with higher Cu concentrations. Shotgun metagenomic sequencing was performed to obtain the gene pool of environmental DNA (eDNA), which was subjected to a local BLAST search against an MT database for detecting putative MT genes. Evolutional trace analysis led to the identification of 27 potential MTs with conserved cysteine/histidine motifs different from those of known prokaryotic MTs. Following chemical synthesis of these 27 potential MT genes and heterologous expression in Escherichia coli, six of them were found to improve the hosts' growth substantially and enhanced the hosts' sorption of Cu, Cd, and Zn, among which MT5 led to a 13.7-fold increase in Cd accumulation. Furthermore, four of them restored Cu and/or Cd resistance in two metal-sensitive E. coli strains.IMPORTANCE The metagenomics-guided procedure developed here bypasses the difficulties encountered in classic PCR-based approaches and led to the discovery of novel MT genes, which may be useful in developing bioremediation tools. The procedure used here expands our knowledge on the diversity of bacterial MTs in the environment and may also be applicable to identify other functional genes from eDNA.
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16
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Tamura K, Foley MH, Gardill BR, Dejean G, Schnizlein M, Bahr CME, Louise Creagh A, van Petegem F, Koropatkin NM, Brumer H. Surface glycan-binding proteins are essential for cereal beta-glucan utilization by the human gut symbiont Bacteroides ovatus. Cell Mol Life Sci 2019; 76:4319-4340. [PMID: 31062073 PMCID: PMC6810844 DOI: 10.1007/s00018-019-03115-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/03/2019] [Accepted: 04/23/2019] [Indexed: 02/07/2023]
Abstract
The human gut microbiota, which underpins nutrition and systemic health, is compositionally sensitive to the availability of complex carbohydrates in the diet. The Bacteroidetes comprise a dominant phylum in the human gut microbiota whose members thrive on dietary and endogenous glycans by employing a diversity of highly specific, multi-gene polysaccharide utilization loci (PUL), which encode a variety of carbohydrases, transporters, and sensor/regulators. PULs invariably also encode surface glycan-binding proteins (SGBPs) that play a central role in saccharide capture at the outer membrane. Here, we present combined biophysical, structural, and in vivo characterization of the two SGBPs encoded by the Bacteroides ovatus mixed-linkage β-glucan utilization locus (MLGUL), thereby elucidating their key roles in the metabolism of this ubiquitous dietary cereal polysaccharide. In particular, molecular insight gained through several crystallographic complexes of SGBP-A and SGBP-B with oligosaccharides reveals that unique shape complementarity of binding platforms underpins specificity for the kinked MLG backbone vis-à-vis linear β-glucans. Reverse-genetic analysis revealed that both the presence and binding ability of the SusD homolog BoSGBPMLG-A are essential for growth on MLG, whereas the divergent, multi-domain BoSGBPMLG-B is dispensable but may assist in oligosaccharide scavenging from the environment. The synthesis of these data illuminates the critical role SGBPs play in concert with other MLGUL components, reveals new structure-function relationships among SGBPs, and provides fundamental knowledge to inform future (meta)genomic, biochemical, and microbiological analyses of the human gut microbiota.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Matthew H Foley
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Bernd R Gardill
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Guillaume Dejean
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Matthew Schnizlein
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Constance M E Bahr
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - A Louise Creagh
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
- Department of Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Filip van Petegem
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada.
- Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Department of Botany, University of British Columbia, 3200 University Boulevard, Vancouver, BC, V6T 1Z4, Canada.
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17
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Rahfeld P, Wardman JF, Mehr K, Huff D, Morgan-Lang C, Chen HM, Hallam SJ, Withers SG. Prospecting for microbial α- N-acetylgalactosaminidases yields a new class of GH31 O-glycanase. J Biol Chem 2019; 294:16400-16415. [PMID: 31530641 DOI: 10.1074/jbc.ra119.010628] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/16/2019] [Indexed: 12/18/2022] Open
Abstract
α-Linked GalNAc (α-GalNAc) is most notably found at the nonreducing terminus of the blood type-determining A-antigen and as the initial point of attachment to the peptide backbone in mucin-type O-glycans. However, despite their ubiquity in saccharolytic microbe-rich environments such as the human gut, relatively few α-N-acetylgalactosaminidases are known. Here, to discover and characterize novel microbial enzymes that hydrolyze α-GalNAc, we screened small-insert libraries containing metagenomic DNA from the human gut microbiome. Using a simple fluorogenic glycoside substrate, we identified and characterized a glycoside hydrolase 109 (GH109) that is active on blood type A-antigen, along with a new subfamily of glycoside hydrolase 31 (GH31) that specifically cleaves the initial α-GalNAc from mucin-type O-glycans. This represents a new activity in this GH family and a potentially useful new enzyme class for analysis or modification of O-glycans on protein or cell surfaces.
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Affiliation(s)
- Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Jacob F Wardman
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada
| | - Kevin Mehr
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Drew Huff
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada.,Graduate Program in Bioinformatics, University of British Columbia, Genome Sciences Centre, Vancouver, British Columbia V5Z 4S6, Canada.,ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.,Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Life Sciences Centre, Vancouver, British Columbia V6T 1Z3, Canada
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18
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Pratama R, Schneider D, Böer T, Daniel R. First Insights Into Bacterial Gastrointestinal Tract Communities of the Eurasian Beaver ( Castor fiber). Front Microbiol 2019; 10:1646. [PMID: 31428060 PMCID: PMC6690062 DOI: 10.3389/fmicb.2019.01646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 07/03/2019] [Indexed: 01/08/2023] Open
Abstract
The Eurasian or European beaver (Castor fiber) is the second-largest living rodent after the capybara. It is a semi-aquatic animal known for building dams and lodges. They strictly feed on lignocellulose-rich plants and correspondingly harbor cellulolytic microbial communities in their digestive tract. In this study, the bacterial community composition, diversity, and functional profile of different gut compartments ranging from stomach to colon have been explored. A total of 277 bacterial operational taxonomic units (OTUs) at species level were obtained from the gut systems of two males (juvenile and subadult) and one subadult female beaver. In general, cecum and colon are dominated by Firmicutes and Actinobacteria. High abundance of Bacteroidetes was observed only in male juvenile beaver cecum and colon, suggesting that the bacterial composition changes with age. Within the cecum and colon, members of known cellulase-producing bacterial taxa including the families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae 1 were detected. The presence of putative genes encoding cellulolytic and carbohydrate-degrading enzymes indicated also the degradation of recalcitrant plant material in both gut compartments. The bacterial community in the gut systems of the Eurasian beaver differed from that of the North American beaver. Higher abundance of Actinobacteria and lower abundances of Bacteroidetes were recorded in the Eurasian beaver. Similar differences were obtained to bacterial communities of termites and herbivorous animals such as bovine. The data presented in this study provides the first insight into bacterial communities in the gut system of the Eurasian beaver.
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Affiliation(s)
- Rahadian Pratama
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
- Department of Biochemistry, Faculty of Mathematics and Natural Sciences, Bogor Agricultural University (IPB University), Bogor, Indonesia
| | - Dominik Schneider
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Tim Böer
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Göttingen Genomics Laboratory, Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany
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19
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Krüger K, Chafee M, Ben Francis T, Glavina Del Rio T, Becher D, Schweder T, Amann RI, Teeling H. In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. ISME JOURNAL 2019; 13:2800-2816. [PMID: 31316134 PMCID: PMC6794258 DOI: 10.1038/s41396-019-0476-y] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/01/2019] [Accepted: 07/04/2019] [Indexed: 11/09/2022]
Abstract
We investigated Bacteroidetes during spring algae blooms in the southern North Sea in 2010–2012 using a time series of 38 deeply sequenced metagenomes. Initial partitioning yielded 6455 bins, from which we extracted 3101 metagenome-assembled genomes (MAGs) including 1286 Bacteroidetes MAGs covering ~120 mostly uncultivated species. We identified 13 dominant, recurrent Bacteroidetes clades carrying a restricted set of conserved polysaccharide utilization loci (PULs) that likely mediate the bulk of bacteroidetal algal polysaccharide degradation. The majority of PULs were predicted to target the diatom storage polysaccharide laminarin, alpha-glucans, alpha-mannose-rich substrates, and sulfated xylans. Metaproteomics at 14 selected points in time revealed expression of SusC-like proteins from PULs targeting all of these substrates. Analyses of abundant key players and their PUL repertoires over time furthermore suggested that fewer and simpler polysaccharides dominated early bloom stages, and that more complex polysaccharides became available as blooms progressed.
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Affiliation(s)
- Karen Krüger
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Meghan Chafee
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - T Ben Francis
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | | | - Dörte Becher
- Institute for Microbiology, University Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Thomas Schweder
- Pharmaceutical Biotechnology, Institute of Pharmacy, University Greifswald, Felix-Hausdorff-Straße 3, 17487, Greifswald, Germany.,Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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20
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High-Throughput Recovery and Characterization of Metagenome-Derived Glycoside Hydrolase-Containing Clones as a Resource for Biocatalyst Development. mSystems 2019; 4:4/4/e00082-19. [PMID: 31164449 PMCID: PMC6550366 DOI: 10.1128/msystems.00082-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans. Functional metagenomics is a powerful tool for both the discovery and development of biocatalysts. This study presents the high-throughput functional screening of 22 large-insert fosmid libraries containing over 300,000 clones sourced from natural and engineered ecosystems, characterization of active clones, and a demonstration of the utility of recovered genes or gene cassettes in the development of novel biocatalysts. Screening was performed in a 384-well-plate format with the fluorogenic substrate 4-methylumbelliferyl cellobioside, which releases a fluorescent molecule when cleaved by β-glucosidases or cellulases. The resulting set of 164 active clones was subsequently interrogated for substrate preference, reaction mechanism, thermal stability, and optimal pH. The environmental DNA harbored within each active clone was sequenced, and functional annotation revealed a cornucopia of carbohydrate-degrading enzymes. Evaluation of genomic-context information revealed both synteny and polymer-targeting loci within a number of sequenced clones. The utility of these fosmids was then demonstrated by identifying clones encoding activity on an unnatural glycoside (4-methylumbelliferyl 6-azido-6-deoxy-β-d-galactoside) and transforming one of the identified enzymes into a glycosynthase capable of forming taggable disaccharides. IMPORTANCE The generation of new biocatalysts for plant biomass degradation and glycan synthesis has typically relied on the characterization and investigation of one or a few enzymes at a time. By coupling functional metagenomic screening and high-throughput functional characterization, we can progress beyond the current scale of catalyst discovery and provide rapid annotation of catalyst function. By functionally screening environmental DNA from many diverse sources, we have generated a suite of active glycoside hydrolase-containing clones and demonstrated their reaction parameters. We then demonstrated the utility of this collection through the generation of a new catalyst for the formation of azido-modified glycans. Further interrogation of this collection of clones will expand our biocatalytic toolbox, with potential application to biomass deconstruction and synthesis of glycans.
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21
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Macdonald SS, Armstrong Z, Morgan-Lang C, Osowiecka M, Robinson K, Hallam SJ, Withers SG. Development and Application of a High-Throughput Functional Metagenomic Screen for Glycoside Phosphorylases. Cell Chem Biol 2019; 26:1001-1012.e5. [PMID: 31080075 DOI: 10.1016/j.chembiol.2019.03.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/15/2019] [Accepted: 03/27/2019] [Indexed: 01/19/2023]
Abstract
Glycoside phosphorylases (GPs) catalyze the reversible phosphorolysis of glycosidic bonds, releasing sugar 1-phosphates. To identify a greater range of these under-appreciated enzymes, we have developed a high-throughput functional screening method based on molybdenum blue formation. In a proof-of-principle screen focused on cellulose-degrading GPs we interrogated ∼23,000 large insert (fosmid) clones sourced from microbial communities inhabiting two separate environments and identified seven novel GPs from carbohydrate active enzyme family GH94 and one from GH149. Characterization identified cellobiose phosphorylases, cellodextrin phosphorylases, laminaribiose phosphorylases, and a β-1,3-glucan phosphorylase. To demonstrate the versatility of the screening method, varying substrate combinations were used to identify GP activity from families GH13, GH65, GH112, and GH130 in addition to GH94 and GH149. These pilot screen and substrate versatility results provide a screening paradigm platform for recovering diverse GPs from uncultivated microbial communities acting on different substrates with considerable potential to unravel previously unknown degradative pathways within microbiomes.
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Affiliation(s)
- Spencer S Macdonald
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Zachary Armstrong
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Connor Morgan-Lang
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Magdalena Osowiecka
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Kyle Robinson
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Steven J Hallam
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Graduate Program in Bioinformatics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Peter Wall Institute for Advanced Studies, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada; Genome Science and Technology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; ECOSCOPE Training Program, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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Bågenholm V, Wiemann M, Reddy SK, Bhattacharya A, Rosengren A, Logan DT, Stålbrand H. A surface-exposed GH26 β-mannanase from Bacteroides ovatus: Structure, role, and phylogenetic analysis of BoMan26B. J Biol Chem 2019; 294:9100-9117. [PMID: 31000630 PMCID: PMC6556568 DOI: 10.1074/jbc.ra118.007171] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/17/2019] [Indexed: 12/27/2022] Open
Abstract
The galactomannan utilization locus (BoManPUL) of the human gut bacterium Bacteroides ovatus encodes BoMan26B, a cell-surface–exposed endomannanase whose functional and structural features have been unclear. Our study now places BoMan26B in context with related enzymes and reveals the structural basis for its specificity. BoMan26B prefers longer substrates and is less restricted by galactose side-groups than the mannanase BoMan26A of the same locus. Using galactomannan, BoMan26B generated a mixture of (galactosyl) manno-oligosaccharides shorter than mannohexaose. Three defined manno-oligosaccharides had affinity for the SusD-like surface–exposed glycan-binding protein, predicted to be implicated in saccharide transport. Co-incubation of BoMan26B and the periplasmic α-galactosidase BoGal36A increased the rate of galactose release by about 10-fold compared with the rate without BoMan26B. The results suggested that BoMan26B performs the initial attack on galactomannan, generating oligosaccharides that after transport to the periplasm are processed by BoGal36A. A crystal structure of BoMan26B with galactosyl-mannotetraose bound in subsites −5 to −2 revealed an open and long active-site cleft with Trp-112 in subsite −5 concluded to be involved in mannosyl interaction. Moreover, Lys-149 in the −4 subsite interacted with the galactosyl side-group of the ligand. A phylogenetic tree consisting of GH26 enzymes revealed four strictly conserved GH26 residues and disclosed that BoMan26A and BoMan26B reside on two distinct phylogenetic branches (A and B). The three other branches contain lichenases, xylanases, or enzymes with unknown activities. Lys-149 is conserved in a narrow part of branch B, and Trp-112 is conserved in a wider group within branch B.
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Affiliation(s)
- Viktoria Bågenholm
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Mathias Wiemann
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Sumitha K Reddy
- the Department of Molecular Sciences, Swedish University of Agricultural Sciences Box 7015, 750 07, Uppsala, Sweden
| | - Abhishek Bhattacharya
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Anna Rosengren
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Derek T Logan
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
| | - Henrik Stålbrand
- From the Department of Biochemistry and Structural Biology, Lund University P. O. Box 124, S-221 00, Lund, Sweden and
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