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Zhang AH, Tang H, Wang L, He W, Gao TH, Gao ZG, Zhang DF. Actomonas aquatica gen. nov., sp. nov., a marine lineage in the phylum Verrucomicrobiota with genetic potential for carbon and nitrogen fixation. Int J Syst Evol Microbiol 2024; 74. [PMID: 38568073 DOI: 10.1099/ijsem.0.006314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024] Open
Abstract
A novel bacterial strain, designated WL0086T, was isolated from a marine sediment sample collected in Lianyungang city, Jiangsu province, PR China. This strain showed the highest 16S rRNA gene sequence similarity to Geminisphaera colitermitum TAV2T (92.7 %) of the family Opitutaceae, and all the unclassified cultured and uncultured isolates with similarities >95 % were from marine environments. Cells were Gram-stain-negative, aerobic, non-motile cocci with a size of 0.6-0.8 µm in diameter. Strain WL0086T was positive for both oxidase and catalase, and grew at 20-37 °C (optimum, 28 °C), with 1.5-11.0 % NaCl (w/v; optimum, 2.5-4.0 %) and at pH 5.0-9.0 (optimum, pH 7.0). The major polar lipid profile of strain WL0086T consisted of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, and phosphatidylcholine. The major isoprenoid quinone was menaquinone-7 and the predominant fatty acids were iso-C14 : 0, anteiso-C15 : 0, C16 : 0 and C16 : 1 ω9c. The complete genome consisted of a chromosome with 6 109 182 bp. The G+C content of genomic DNA was 64.0%. Results of phylogenomic analysis based on the 16S rRNA gene sequence and the whole genome suggested that strain WL0086T formed a distinct clade closely neighbouring the members of the family Opitutaceae. On the basis of phylogenetic, phenotypic, and chemotaxonomic evidences, strain WL0086T should represent a novel genus of the family Opitutaceae, for which the name Actomonas aquatica gen. nov., sp. nov. is proposed. The type strain is WL0086T (=MCCC 1K05844T=JCM 34677T=GDMCC 1.2411T).
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Affiliation(s)
- Ai Hua Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, Jiangsu, PR China
| | - Hao Tang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, Jiangsu, PR China
| | - Lu Wang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, Jiangsu, PR China
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, PR China
| | - Wei He
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, Jiangsu, PR China
| | - Tian Heng Gao
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, Jiangsu, PR China
- Jiangsu Province Engineering Research Center for Aquatic Animals Breeding and Green Efficient Aquacultural Technology, College of Marine Science and Engineering, Nanjing Normal University, Nanjing, 210023, PR China
| | - Zhi Gang Gao
- Dongtai Cibainian Bioengineering Company Limited, Yancheng 224200, PR China
| | - Dao-Feng Zhang
- Jiangsu Province Engineering Research Center for Marine Bio-resources Sustainable Utilization & College of Oceanography, Hohai University, Nanjing 210024, Jiangsu, PR China
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Padilla L, Fricker AD, Luna E, Choudhury B, Hughes ER, Panzetta ME, Valdivia RH, Flores GE. Mechanism of 2'-fucosyllactose degradation by human-associated Akkermansia. J Bacteriol 2024; 206:e0033423. [PMID: 38299857 PMCID: PMC10886448 DOI: 10.1128/jb.00334-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 01/04/2024] [Indexed: 02/02/2024] Open
Abstract
Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2'-fucosyllactose (2'-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2'-FL. In culture, we found growth of two species, A. muciniphila MucT and A. biwaensis CSUN-19,on HMOs corresponded to a decrease in the levels of 2'-FL and an increase in lactose, indicating that the first step in 2'-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, vary between these two species. During the mid-log phase of growth, the expression of several GH29 genes was increased by 2'-FL in both species, whereas the GH95 genes were induced only in A. muciniphila. We further show that one putative fucosidase and a β-galactosidase from A. biwaensis are involved in the breakdown of 2'-FL. Our findings indicate that the plasticity of GHs of human-associated Akkermansia sp. enables access to additional growth substrates present in HMOs, including 2'-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont.IMPORTANCEAkkermansia are mucin-degrading specialists widely distributed in the human population. Akkermansia biwaensis has recently been observed to have enhanced growth relative to other human-associated Akkermansia on multiple human milk oligosaccharides (HMOs). However, the mechanisms for enhanced growth are not understood. Here, we characterized the phylogenetic diversity and function of select genes involved in the growth of A. biwaensis on 2'-fucosyllactose (2'-FL), a dominant HMO. Specifically, we demonstrate that two genes in a genomic locus, a putative β-galactosidase and α-fucosidase, are likely responsible for the enhanced growth on 2'-FL. The functional characterization of A. biwaensis growth on 2'-FL delineates the significance of a single genomic locus that may facilitate enhanced colonization and functional activity of select Akkermansia early in life.
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Affiliation(s)
- Loren Padilla
- Department of Biology, California State University, Northridge, California, USA
| | - Ashwana D. Fricker
- Department of Biology, California State University, Northridge, California, USA
| | - Estefani Luna
- Department of Biology, California State University, Northridge, California, USA
| | - Biswa Choudhury
- GlycoAnalytics Core, UC San Diego, Health Sciences, La Jolla, California, USA
| | - Elizabeth R. Hughes
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maria E. Panzetta
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Raphael H. Valdivia
- Department of Integrative Immunobiology, Duke University School of Medicine, Durham, North Carolina, USA
| | - Gilberto E. Flores
- Department of Biology, California State University, Northridge, California, USA
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Wu W, Zhao Z, Zhao Z, Zhang D, Zhang Q, Zhang J, Fang Z, Bai Y, Guo X. Structure, Health Benefits, Mechanisms, and Gut Microbiota of Dendrobium officinale Polysaccharides: A Review. Nutrients 2023; 15:4901. [PMID: 38068759 PMCID: PMC10708504 DOI: 10.3390/nu15234901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Dendrobium officinale polysaccharides (DOPs) are important active polysaccharides found in Dendrobium officinale, which is commonly used as a conventional food or herbal medicine and is well known in China. DOPs can influence the composition of the gut microbiota and the degradation capacity of these symbiotic bacteria, which in turn may determine the efficacy of dietary interventions. However, the necessary analysis of the relationship between DOPs and the gut microbiota is lacking. In this review, we summarize the extraction, structure, health benefits, and related mechanisms of DOPs, construct the DOPs-host axis, and propose that DOPs are potential prebiotics, mainly composed of 1,4-β-D-mannose, 1,4-β-D-glucose, and O-acetate groups, which induce an increase in the abundance of gut microbiota such as Lactobacillus, Bifidobacterium, Akkermansia, Bacteroides, and Prevotella. In addition, we found that when exposed to DOPs with different structural properties, the gut microbiota may exhibit different diversity and composition and provide health benefits, such as metabolism regulations, inflammation modulation, immunity moderation, and cancer intervention. This may contribute to facilitating the development of functional foods and health products to improve human health.
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Affiliation(s)
- Weijie Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (W.W.); (Z.Z.); (Z.Z.); (D.Z.); (Q.Z.); (Y.B.)
| | - Ziqi Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (W.W.); (Z.Z.); (Z.Z.); (D.Z.); (Q.Z.); (Y.B.)
| | - Zhaoer Zhao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (W.W.); (Z.Z.); (Z.Z.); (D.Z.); (Q.Z.); (Y.B.)
| | - Dandan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (W.W.); (Z.Z.); (Z.Z.); (D.Z.); (Q.Z.); (Y.B.)
| | - Qianyi Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (W.W.); (Z.Z.); (Z.Z.); (D.Z.); (Q.Z.); (Y.B.)
| | - Jiayu Zhang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China;
| | - Zhengyi Fang
- School of Clinical Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China;
| | - Yiling Bai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (W.W.); (Z.Z.); (Z.Z.); (D.Z.); (Q.Z.); (Y.B.)
| | - Xiaohui Guo
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (W.W.); (Z.Z.); (Z.Z.); (D.Z.); (Q.Z.); (Y.B.)
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Padilla L, Fricker AD, Luna E, Choudhury B, Hughes ER, Panzetta ME, Valdivia RH, Flores GE. Mechanism of 2'-Fucosyllactose degradation by Human-Associated Akkermansia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562767. [PMID: 37904935 PMCID: PMC10614881 DOI: 10.1101/2023.10.17.562767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Among the first microorganisms to colonize the human gut of breastfed infants are bacteria capable of fermenting human milk oligosaccharides (HMOs). One of the most abundant HMOs, 2'-fucosyllactose (2'-FL), may specifically drive bacterial colonization of the intestine. Recently, differential growth has been observed across multiple species of Akkermansia on various HMOs including 2'FL. In culture, we found growth of two species, A. muciniphila Muc T and A. biwaensis CSUN-19, in HMOS corresponded to a decrease in the levels of 2'-FL and an increase in lactose, indicating that the first step in 2'-FL catabolism is the cleavage of fucose. Using phylogenetic analysis and transcriptional profiling, we found that the number and expression of fucosidase genes from two glycoside hydrolase (GH) families, GH29 and GH95, varies between these two species. During mid-log phase growth, the expression of several GH29 genes was increased by 2'-FL in both species, whereas the GH95 genes were induced only in A. muciniphila . We further show that one putative fucosidase and a β-galactosidase from A. biwaensis are involved in the breakdown of 2'-FL. Our findings indicate that that plasticity of GHs of human associated Akkermansia sp. enable access to additional growth substrates present in HMOs, including 2'-FL. Our work highlights the potential for Akkermansia to influence the development of the gut microbiota early in life and expands the known metabolic capabilities of this important human symbiont. IMPORTANCE Akkermansia are mucin degrading specialists widely distributed in the human population. Akkermansia biwaensis has recently been observed to have enhanced growth relative to other human associated Akkermansia on multiple human milk oligosaccharides (HMOs). However, the mechanisms for enhanced growth are not understood. Here, we characterized the phylogenetic diversity and function of select genes involved in growth of A. biwaensis on 2'-fucosyllactose (2'-FL), a dominant HMO. Specifically, we demonstrate that two genes in a genomic locus, a putative β-galactosidase and α-fucosidase, are likely responsible for the enhanced growth on 2'-FL. The functional characterization of A. biwaensis growth on 2'-FL delineates the significance of a single genomic locus that may facilitate enhanced colonization and functional activity of select Akkermansia early in life.
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