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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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Complete Genome Sequence of Klebsiella sp. CTHL.F3a, a Cellulolytic Strain Isolated from Korean Kimchi. Microbiol Resour Announc 2022; 11:e0037722. [PMID: 35862935 PMCID: PMC9387283 DOI: 10.1128/mra.00377-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The cellulolytic strain Klebsiella sp. CTHL.F3a was isolated from kimchi (Korean fermented cabbage/vegetables). Its complete genome sequence (6,146,223 bp, GC content of 55.21%), comprising a chromosome and a single plasmid, was established through hybrid assembly.
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Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats. THE ISME JOURNAL 2022; 16:1980-1992. [PMID: 35568757 PMCID: PMC9107070 DOI: 10.1038/s41396-022-01247-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 11/29/2022]
Abstract
Bamboo rats (Rhizomys pruinosus) are among the few mammals that lives on a bamboo-based diet which is mainly composed of lignocellulose. However, the mechanisms of adaptation of their gut microbiome and metabolic systems in the degradation of lignocellulose are largely unknown. Here, we conducted a multi-omics analysis on bamboo rats to investigate the interaction between their gut microbiomes and metabolic systems in the pre- and post-weaning periods, and observed significant relationships between dietary types, gut microbiome, serum metabolome and host gene expression. For comparison, published gut microbial data from the famous bamboo-eating giant panda (Ailuropoda melanoleuca) were also used for analysis. We found that the adaptation of the gut microbiome of the bamboo rat to a lignocellulose diet is related to a member switch in the order Bacteroidales from family Bacteroidaceae to family Muribaculaceae, while for the famous bamboo-eating giant panda, several aerobes and facultative anaerobes increase after weaning. The conversion of bacteria with an increased relative abundance in bamboo rats after weaning enriched diverse carbohydrate-active enzymes (CAZymes) associated with lignocellulose degradation and functionally enhanced the biosynthesis of amino acids and B vitamins. Meanwhile, the circulating concentration of short-chain fatty acids (SCFAs) derived metabolites and the metabolic capacity of linoleic acid in the host were significantly elevated. Our findings suggest that fatty acid metabolism, including linoleic acid and SCFAs, are the main energy sources for bamboo rats in response to the low-nutrient bamboo diet.
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Zhan M, Wang A, Yao Y, Zhou Y, Zhang S, Fu X, Zhou J, Pei E, Wang L. An amateur gut microbial configuration formed in giant panda for striving to digest cellulose in bamboo: Systematic evidence from intestinal digestive enzymes, functional genes and microbial structures. Front Microbiol 2022; 13:926515. [PMID: 35958139 PMCID: PMC9363027 DOI: 10.3389/fmicb.2022.926515] [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: 04/22/2022] [Accepted: 07/04/2022] [Indexed: 11/14/2022] Open
Abstract
The giant panda has been considered to maximize nutritional intake including protein and soluble carbohydrates in bamboo, but it has spent almost entire life with the high-cellulose diet. Whether giant panda is still helpless about digesting bamboo cellulose or not is always contentious among many researchers around the world. The work has systematically clarified this issue from the perspectives of digestive enzymes, functional genes, and microbial structures in giant panda gut. The intestinal cellulase activities of panda increase with bamboo consumption, performing that the endoglucanase activity of adults reaches 10-fold that of pandas first consuming bamboo. More abundance and types of microbial endoglucanase genes occur in bamboo-diet giant panda gut, and the corresponding GH5 gene cluster is still efficiently transcribed. Gut microbes possessing cellulose-degrading genes, belong to the phylum Firmicutes and some Bacteroidetes, but their structural and functional configurations are insufficient to completely degrade cellulose. Therefore, giant panda is striving to digest cellulose in bamboo, but this adaptation is incomplete. This is probably related to the short straight carnivore-like gut structure of the giant panda, preventing the colonization of some efficient functional but anaerobic-preferred flora.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Center for the Giant Panda, Dujiangyan, China
| | | | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
- *Correspondence: Lei Wang,
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Bai DP, Lin XY, Hu YQ, Chen ZZ, Chen L, Huang YF, Huang XH, Li J. Metagenomics approach to identify lignocellulose-degrading enzymes in the gut microbiota of the Chinese bamboo rat cecum. ELECTRON J BIOTECHN 2021. [DOI: 10.1016/j.ejbt.2020.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Zhan M, Wang L, Xie C, Fu X, Zhang S, Wang A, Zhou Y, Xu C, Zhang H. Succession of Gut Microbial Structure in Twin Giant Pandas During the Dietary Change Stage and Its Role in Polysaccharide Metabolism. Front Microbiol 2020; 11:551038. [PMID: 33072012 PMCID: PMC7537565 DOI: 10.3389/fmicb.2020.551038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 08/27/2020] [Indexed: 12/23/2022] Open
Abstract
Adaptation to a bamboo diet is an essential process for giant panda growth, and gut microbes play an important role in the digestion of the polysaccharides in bamboo. The dietary transition in giant panda cubs is particularly complex, but it is an ideal period in which to study the effects of gut microbes on polysaccharide use because their main food changes from milk to bamboo (together with some bamboo shoot and coarse pastry). Here, we used 16S rDNA and internal transcribed spacer 1 (ITS1) DNA sequencing and metagenomic sequencing analysis to investigate the succession of the gut microbial structure in feces sampled from twin giant panda cubs during the completely dietary transition and determine the abundances of polysaccharide-metabolizing genes and their corresponding microbes to better understand the degradation of bamboo polysaccharides. Successive changes in the gut microbial diversity and structure were apparent in the growth of pandas during dietary shift process. Microbial diversity increased after the introduction of supplementary foods and then varied in a complex way for 1.5–2 years as bamboo and complex food components were introduced. They then stabilized after 2 years, when the cubs consumed a specialized bamboo diet. The microbes had more potential to metabolize the cellulose in bamboo than the hemicellulose, providing genes encoding cellulase systems corresponding to glycoside hydrolases (GHs; such as GH1, GH3, GH5, GH8, GH9, GH74, and GH94). The cellulose-metabolizing species (or genes) of gut bacteria was more abundant than that of gut fungi. Although cellulose-metabolizing species did not predominate in the gut bacterial community, microbial interactions allowed the giant pandas to achieve the necessary dietary shift and ultimately adapt to a bamboo diet.
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Affiliation(s)
- Mingye Zhan
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Lei Wang
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | - Chunyu Xie
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Xiaohua Fu
- College of Environmental Science and Engineering, Institute of Pollution Control and Ecological Safety, Tongji University, Shanghai, China
| | | | | | - Yingmin Zhou
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
| | - Chunzhong Xu
- Shanghai Wild Animal Park Development Co., Ltd., Shanghai, China
| | - Hemin Zhang
- China Conservation and Research Centre for the Giant Panda, Dujiangyan, China
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Li Y, Li R, Yu H, Sheng X, Wang J, Fisher AJ, Chen X. Enterococcus faecalis α1-2-mannosidase (EfMan-I): an efficient catalyst for glycoprotein N-glycan modification. FEBS Lett 2019; 594:439-451. [PMID: 31552675 DOI: 10.1002/1873-3468.13618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 09/18/2019] [Accepted: 09/19/2019] [Indexed: 01/08/2023]
Abstract
While multiple α 1-2-mannosidases are necessary for glycoprotein N-glycan maturation in vertebrates, a single bacterial α1-2-mannosidase can be sufficient to cleave all α1-2-linked mannose residues in host glycoprotein N-glycans. We report here the characterization and crystal structure of a new α1-2-mannosidase (EfMan-I) from Enterococcus faecalis, a Gram-positive opportunistic human pathogen. EfMan-I catalyzes the cleavage of α1-2-mannose from not only oligomannoses but also high-mannose-type N-glycans on glycoproteins. Its 2.15 Å resolution crystal structure reveals a two-domain enzyme fold similar to other CAZy GH92 mannosidases. An unexpected potassium ion was observed bridging two domains near the active site. These findings support EfMan-I as an effective catalyst for in vitro N-glycan modification of glycoproteins with high-mannose-type N-glycans.
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Affiliation(s)
- Yanhong Li
- Department of Chemistry, University of California, Davis, CA, USA
| | - Riyao Li
- Department of Chemistry, University of California, Davis, CA, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, CA, USA
| | - Xue Sheng
- Department of Chemistry, University of California, Davis, CA, USA
| | - Jing Wang
- Department of Chemistry, University of California, Davis, CA, USA.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Andrew J Fisher
- Department of Chemistry, University of California, Davis, CA, USA.,Department of Molecular and Cellular Biology, University of California, Davis, CA, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA, USA
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