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Gajera G, Funde S, Palep H, Kothari V. Duration of fermentation affects microbiome composition and biological activity of an Indian traditional formulation - Panchagavya. J Ayurveda Integr Med 2024; 15:100880. [PMID: 38457966 PMCID: PMC10940934 DOI: 10.1016/j.jaim.2023.100880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 12/08/2023] [Accepted: 12/14/2023] [Indexed: 03/10/2024] Open
Abstract
OBJECTIVE This study aimed at investigating whether the duration of fermenting Panchagavya (PG) preparation in copper vessel affects its biological activity and microbiome composition. MATERIALS AND METHODS Prophylactic potential of PG against bacterial infection was assessed through an in vivo assay employing the nematode worm Caenorhabditis elegans as a model host. Bacterial diversity of the PG samples was revealed through metagenomic analysis. RESULTS Duration of fermentation was found to affect biological activity as well as microbiome composition of the PG samples. PG-samples fermented ≥60 min lost their prophylactic potential, and develop anthelmintic activity. Bacterial phyla whose relative abundance was significantly different between the prophylactic and anthelmintic PG samples were Planctomycetota, Proteabacteria, Bacteroidota, Verrucomicrobiota, Patescibacteria, Acidobacteriota, Chloroflexi, Firmicutes and Campilobacterota. CONCLUSION This study validates the prophylactic potential of Panchagavya against bacterial pathogens, and shows that duration of the fermentation time while preparing PG can have profound effect on its biological activities. Biological activities of PG samples seem to have a correlation with their inherent microbial community. Metagenomic profiling can be an effective tool for standardization of PG formulations.
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Affiliation(s)
- Gemini Gajera
- Institute of Science, Nirma University, Ahmedabad, 382481, India
| | - Snehal Funde
- Dr. Palep's Medical Research Foundation, Mumbai, India
| | | | - Vijay Kothari
- Institute of Science, Nirma University, Ahmedabad, 382481, India.
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Rekadwad BN, Shouche YS, Jangid K. Investigation of tRNA-based relatedness within the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) superphylum: a comparative analysis. Arch Microbiol 2023; 205:366. [PMID: 37917352 DOI: 10.1007/s00203-023-03694-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 11/04/2023]
Abstract
The PVC superphylum is a diverse group of prokaryotes that require stringent growth conditions. RNA is a fascinating molecule to find evolutionary relatedness according to the RNA World Hypothesis. We conducted tRNA gene analysis to find evolutionary relationships in the PVC phyla. The analysis of genomic data (P = 9, V = 4, C = 8) revealed that the number of tRNA genes varied from 28 to 90 in Planctomycetes and Chlamydia, respectively. Verrucomicrobia has whole genomes and the longest scaffold (3 + 1), with tRNA genes ranging from 49 to 53 in whole genomes and 4 in the longest scaffold. Most tRNAs in the E. coli genome clustered with homologs, but approximately 43% clustered with tRNAs encoding different amino acids. Planctomyces, Akkermansia, Isosphaera, and Chlamydia were similar to E. coli tRNAs. In a phylum, tRNAs coding for different amino acids clustered at a range of 8 to 10%. Further analysis of these tRNAs showed sequence similarity with Cyanobacteria, Proteobacteria, Viridiplantae, Ascomycota and Basidiomycota (Eukaryota). This indicates the possibility of horizontal gene transfer or, otherwise, a different origin of tRNA in PVC bacteria. Hence, this work proves its importance for determining evolutionary relatedness and potentially identifying bacteria using tRNA. Thus, the analysis of these tRNAs indicates that primitive RNA may have served as the genetic material of LUCA before being replaced by DNA. A quantitative analysis is required to test these possibilities that relate the evolutionary significance of tRNA to the origin of life.
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Affiliation(s)
- Bhagwan Narayan Rekadwad
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India.
- Microbe AI Lab, Division of Microbiology and Biotechnology, Yenepoya Research Centre, Yenepoya (Deemed to Be University), Mangalore, 575018, Karnataka, India.
| | - Yogesh S Shouche
- National Centre for Microbial Resource (NCMR), DBT-National Centre for Cell Science (DBT-NCCS), Saviribai Phule Pune University Campus, Ganeshkhind, Pune, 411007, Maharashtra, India
- Gut Microbiology Research Division, SKAN Research Trust, Bangalore, 560034, Karnataka, India
| | - Kamlesh Jangid
- Bioenergy Group, DST-Agharkar Research Institute, Gopal Ganesh Agarkar Road, Pune, 411004, Maharashtra, India
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Lodha T, Narvekar S, Karodi P. Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua. Syst Appl Microbiol 2021; 44:126272. [PMID: 34735804 DOI: 10.1016/j.syapm.2021.126272] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.
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Affiliation(s)
- Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India.
| | - Simran Narvekar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
| | - Prachi Karodi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
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4
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Peeters SH, Wiegand S, Kallscheuer N, Jogler M, Heuer A, Jetten MSM, Boedeker C, Rohde M, Jogler C. Description of Polystyrenella longa gen. nov., sp. nov., isolated from polystyrene particles incubated in the Baltic Sea. Antonie Van Leeuwenhoek 2020; 113:1851-1862. [PMID: 32239304 PMCID: PMC7716846 DOI: 10.1007/s10482-020-01406-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/15/2020] [Indexed: 11/28/2022]
Abstract
Planctomycetes occur in almost all aquatic ecosystems on earth. They have a remarkable cell biology, and members of the orders Planctomycetales and Pirellulales feature cell division by polar budding, perform a lifestyle switch from sessile to motile cells and have an enlarged periplasmic space. Here, we characterise a novel planctomycetal strain, Pla110T, isolated from the surface of polystyrene particles incubated in the Baltic Sea. After phylogenetic analysis, the strain could be placed in the family Planctomycetaceae. Strain Pla110T performs cell division by budding, has crateriform structures and grows in aggregates or rosettes. The strain is a chemoheterotroph, grows under mesophilic and neutrophilic conditions, and exhibited a doubling time of 21 h. Based on our phylogenetic and morphological characterisation, strain Pla110T (DSM 103387T = LMG 29693T) is concluded to represent a novel species belonging to a novel genus, for which we propose the name Polystyrenella longa gen. nov., sp. nov.
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Affiliation(s)
- Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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5
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Peeters SH, Wiegand S, Kallscheuer N, Jogler M, Heuer A, Jetten MSM, Boedeker C, Rohde M, Jogler C. Lignipirellula cremea gen. nov., sp. nov., a planctomycete isolated from wood particles in a brackish river estuary. Antonie Van Leeuwenhoek 2020; 113:1863-1875. [PMID: 32239303 PMCID: PMC7717058 DOI: 10.1007/s10482-020-01407-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/15/2020] [Indexed: 02/07/2023]
Abstract
A novel planctomycetal strain, designated Pla85_3_4T, was isolated from the surface of wood incubated at the discharge of a wastewater treatment plant in the Warnow river near Rostock, Germany. Cells of the novel strain have a cell envelope architecture resembling that of Gram-negative bacteria, are round to pear-shaped (length: 2.2 ± 0.4 µm, width: 1.2 ± 0.3 µm), form aggregates and divide by polar budding. Colonies have a cream colour. Strain Pla85_3_4T grows at ranges of 10-30 °C (optimum 26 °C) and at pH 6.5-10.0 (optimum 7.5), and has a doubling time of 26 h. Phylogenetically, strain Pla85_3_4T (DSM 103796T = LMG 29741T) is concluded to represent a novel species of a novel genus within the family Pirellulaceae, for which we propose the name Lignipirellula cremea gen. nov., sp. nov.
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Affiliation(s)
- Stijn H Peeters
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | | | - Mareike Jogler
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany
| | - Anja Heuer
- Leibniz Institute DSMZ, Brunswick, Germany
| | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands
| | | | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit, Nijmegen, The Netherlands.
- Department of Microbial Interactions, Institute of Microbiology, Friedrich Schiller University, Jena, Germany.
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Boersma AS, Kallscheuer N, Wiegand S, Rast P, Peeters SH, Mesman RJ, Heuer A, Boedeker C, Jetten MSM, Rohde M, Jogler M, Jogler C. Alienimonas californiensis gen. nov. sp. nov., a novel Planctomycete isolated from the kelp forest in Monterey Bay. Antonie Van Leeuwenhoek 2020; 113:1751-1766. [PMID: 31802338 DOI: 10.1007/s10482-019-01367-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/26/2019] [Indexed: 11/26/2022]
Abstract
Planctomycetes are environmentally and biotechnologically important bacteria and are often found in association with nutrient-rich (marine) surfaces. To allow a more comprehensive understanding of planctomycetal lifestyle and physiology we aimed at expanding the collection of axenic cultures with new isolates. Here, we describe the isolation and genomic and physiological characterisation of strain CA12T obtained from giant bladder kelp (Macrocystis pyrifera) in Monterey Bay, California, USA. 16S rRNA gene sequence and whole genome-based phylogenetic analysis showed that strain CA12T clusters within the family Planctomycetaceae and that it has a high 16S rRNA sequence similarity (82.3%) to Planctomicrobium piriforme DSM 26348T. The genome of strain CA12T has a length of 5,475,215 bp and a G+C content of 70.1%. The highest growth rates were observed at 27 °C and pH 7.5. Using different microscopic methods, we could show that CA12T is able to divide by consecutive polar budding, without completing a characteristic planctomycetal lifestyle switch. Based on our data, we suggest that the isolated strain represents a novel species within a novel genus. We thus propose the name Alienimonas gen. nov. with Alienimonas californiensis sp. nov. as type species of the novel genus and CA12T as type strain of the novel species.
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Affiliation(s)
- Alje S Boersma
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Nicolai Kallscheuer
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sandra Wiegand
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Patrick Rast
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | - Stijn H Peeters
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Rob J Mesman
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Mareike Jogler
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
- Leibniz Institute DSMZ Braunschweig, Brunswick, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands.
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Kallscheuer N, Jogler M, Wiegand S, Peeters SH, Heuer A, Boedeker C, Jetten MSM, Rohde M, Jogler C. Rubinisphaera italica sp. nov. isolated from a hydrothermal area in the Tyrrhenian Sea close to the volcanic island Panarea. Antonie Van Leeuwenhoek 2020; 113:1727-1736. [PMID: 31773447 PMCID: PMC7717053 DOI: 10.1007/s10482-019-01329-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/09/2019] [Indexed: 01/09/2023]
Abstract
Planctomycetes is a fascinating phylum of mostly aquatic bacteria, not only due to the environmental importance in global carbon and nitrogen cycles, but also because of a unique cell biology. Their lifestyle and metabolic capabilities are not well explored, which motivated us to study the role of Planctomycetes in biofilms on marine biotic surfaces. Here, we describe the novel strain Pan54T which was isolated from algae in a hydrothermal area close to the volcanic island Panarea in the Tyrrhenian Sea, north of Sicily in Italy. The strain grew best at pH 9.0 and 26 °C and showed typical characteristics of planctomycetal bacteria, e.g. division by polar budding, formation of aggregates and presence of stalks and crateriform structures. Phylogenetically, the strain belongs to the genus Rubinisphaera. Our analysis suggests that Pan54T represents a novel species of this genus, for which we propose the name Rubinisphaera italica sp. nov. We suggest Pan54T (= DSM 29369 = LMG 29789) as the type strain of the novel species.
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Affiliation(s)
- Nicolai Kallscheuer
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Mareike Jogler
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
- Leibniz Institute DSMZ, Braunschweig, Germany
| | - Sandra Wiegand
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Stijn H Peeters
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Anja Heuer
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Mike S M Jetten
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, HZI, Braunschweig, Germany
| | - Christian Jogler
- Department of Microbiology, Radboud Universiteit Nijmegen, Nijmegen, The Netherlands.
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Bringing the diversity of Planctomycetes into the light: Introduction to papers from the special issue on novel taxa of Planctomycetes. Antonie van Leeuwenhoek 2020; 113:1715-1726. [PMID: 33258053 DOI: 10.1007/s10482-020-01499-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/11/2020] [Indexed: 01/21/2023]
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Description of the novel planctomycetal genus Bremerella, containing Bremerella volcania sp. nov., isolated from an active volcanic site, and reclassification of Blastopirellula cremea as Bremerella cremea comb. nov. Antonie van Leeuwenhoek 2020; 113:1823-1837. [DOI: 10.1007/s10482-019-01378-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/12/2019] [Indexed: 02/07/2023]
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10
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Three novel Rubripirellula species isolated from plastic particles submerged in the Baltic Sea and the estuary of the river Warnow in northern Germany. Antonie van Leeuwenhoek 2019; 113:1767-1778. [DOI: 10.1007/s10482-019-01368-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022]
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Chen X, Wang J, Liu M, Yang W, Wang Y, Tang R, Zhang M. Crystallographic evidence for substrate-assisted catalysis of β-N-acetylhexosaminidas from Akkermansia muciniphila. Biochem Biophys Res Commun 2019; 511:833-839. [PMID: 30846208 DOI: 10.1016/j.bbrc.2019.02.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 02/14/2019] [Indexed: 12/21/2022]
Abstract
β-N-acetylhexosaminidases from Akkermansia muciniphila was reported to perform the crystal structure with GlcNAc complex, which proved to be the substrate of Am2301. Domain II of Am2301 is consisted of amino acid residues 111-489 and is folded as a (β/α)8 barrel with the active site combined of the glycosyl hydrolases. Crystallographic evidence showed that Asp-278 and Glu-279 could be the catalytic site and Tyr-373 may plays a role on binding the substrate. Moreover, Am2301 prefers to bind Zn ion, which similar to other GH 20 family. Enzyme activity and kinetic parameters of wild-type Am2301 and mutants proved that Asp-278 and Glu-279 are the catalytic sites and they play a critical role on the catalytic process. Overall, our results demonstrate that Am2301 and its complex with GlcNAC provide obvious structural evidence for substrate-assisted catalysis. Obviously, this expands our understanding on the mode of substrate-assisted reaction for this enzyme family in Akkermansia muciniphila.
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Affiliation(s)
- Xi Chen
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Department of Biological and Food Engineering, Bozhou University, 2266 Tangwang Road, Bozhou, Anhui, China
| | - Junchao Wang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Mingjie Liu
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Wenyi Yang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Yongzhong Wang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China
| | - Rupei Tang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.
| | - Min Zhang
- School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.
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Storesund JE, Lanzèn A, García-Moyano A, Reysenbach AL, Øvreås L. Diversity patterns and isolation of Planctomycetes associated with metalliferous deposits from hydrothermal vent fields along the Valu Fa Ridge (SW Pacific). Antonie van Leeuwenhoek 2018; 111:841-858. [PMID: 29423768 DOI: 10.1007/s10482-018-1026-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 01/25/2018] [Indexed: 02/06/2023]
Abstract
The microbial diversity associated with diffuse venting deep-sea hydrothermal deposits is tightly coupled to the geochemistry of the hydrothermal fluids. Previous 16S rRNA gene amplicon sequencing (metabarcoding) of marine iron-hydroxide deposits along the Arctic Mid Ocean Ridge, revealed the presence of diverse bacterial communities associated with these deposits (Storesund and Øvreås in Antonie van Leeuwenhoek 104:569-584, 2013). One of the most abundant and diverse phyla detected was the enigmatic Planctomycetes. Here we report on the comparative analyses of the diversity and distribution patterns of Planctomycetes associated with metalliferous deposits from two diffuse-flow hydrothermal vent fields (Mariner and Vai Lili) from the Valu Fa Ridge in the Southwestern Pacific. Metabarcoding of 16S rRNA genes showed that the major prokaryotic phyla were Proteobacteria (51-73% of all 16S rRNA gene reads), Epsilonbacteraeota (0.5-19%), Bacteriodetes (5-17%), Planctomycetes (0.4-11%), Candidatus Latescibacteria (0-5%) and Marine Benthic Group E (Hydrothermarchaeota) (0-5%). The two different sampling sites differed considerably in overall community composition. The abundance of Planctomycetes also varied substantially between the samples and the sites, with the majority of the sequences affiliated with uncultivated members of the classes Planctomycetacia and Phycisphaerae, and other deep branching lineages. Seven different strains affiliated with the order Planctomycetales were isolated, mostly from the Vai Lili samples, where also the highest Planctomycetales diversity was seen. Most of the isolates were affiliated with the genera Gimesia, Rhodopirellula and Blastopirellula. One isolate was only distantly related to known cultured, but uncharacterized species within the Pir4 group. This study shows that the deep-sea Planctomycetes represent a very heterogeneous group with a high phylogenetic diversity and a substantial potential for novel organism discovery in these deep ocean environments.
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Affiliation(s)
- Julia Endresen Storesund
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway
| | - Anders Lanzèn
- AZTI, Marine Research Division, Herrera Kaia, Portualdea s/n, 20110, Pasaia, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
| | - Antonio García-Moyano
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway
| | | | - Lise Øvreås
- Department of Biological Sciences, University of Bergen, Thormøhlensgate 53B, Postboks 7803, 5006, Bergen, Norway.
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Rivas-Marín E, Devos DP. The Paradigms They Are a-Changin': past, present and future of PVC bacteria research. Antonie van Leeuwenhoek 2017; 111:785-799. [PMID: 29058138 PMCID: PMC5945725 DOI: 10.1007/s10482-017-0962-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/10/2017] [Indexed: 11/22/2022]
Abstract
These are exciting times for PVC researchers! The PVC superphylum is composed of the bacterial phyla Planctomycetes, Verrucomicrobia, Chlamydiae (those three founders giving it its name), Lentisphaerae and Kirimatiellaeota as well as some uncultured candidate phyla, such as the Candidatus Omnitrophica (previously known as OP3). Despite early debates, most of the disagreements that surround this group of bacteria have been recently resolved. In this article, we review the history of the study of PVC bacteria, with a particular focus on the misinterpretations that emerged early in the field and their resolution. We begin with a historical perspective that describes the relevant facts of PVC research from the early times when they were not yet termed PVC. Those were controversial times and we refer to them as the “discovery age” of the field. We continue by describing new discoveries due to novel techniques and data that combined with the reinterpretations of old ones have contributed to solve most of the discordances and we refer to these times as the “illumination age” of PVC research. We follow by arguing that we are just entering the “golden age” of PVC research and that the future of this growing community is looking bright. We finish by suggesting a few of the directions that PVC researches might take in the future.
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Affiliation(s)
- Elena Rivas-Marín
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, University Pablo de Olavide, Carretera Utrera, km 1, 41013, Seville, Spain.
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Jeske O, Schüler M, Schumann P, Schneider A, Boedeker C, Jogler M, Bollschweiler D, Rohde M, Mayer C, Engelhardt H, Spring S, Jogler C. Planctomycetes do possess a peptidoglycan cell wall. Nat Commun 2015; 6:7116. [PMID: 25964217 PMCID: PMC4432640 DOI: 10.1038/ncomms8116] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 04/07/2015] [Indexed: 11/28/2022] Open
Abstract
Most bacteria contain a peptidoglycan (PG) cell wall, which is critical for
maintenance of shape and important for cell division. In contrast, Planctomycetes
have been proposed to produce a proteinaceous cell wall devoid of PG. The apparent
absence of PG has been used as an argument for the putative planctomycetal ancestry
of all bacterial lineages. Here we show, employing multiple bioinformatic methods,
that planctomycetal genomes encode proteins required for PG synthesis. Furthermore,
we biochemically demonstrate the presence of the sugar and the peptide components of
PG in Planctomycetes. In addition, light and electron microscopic experiments reveal
planctomycetal PG sacculi that are susceptible to lysozyme treatment. Finally,
cryo-electron tomography demonstrates that Planctomycetes possess a typical PG cell
wall and that their cellular architecture is thus more similar to that of other
Gram-negative bacteria. Our findings shed new light on the cellular architecture and
cell division of the maverick Planctomycetes. Planctomycetes appear to differ from all other bacteria in their
cellular organization and their apparent lack of a peptidoglycan (PG) cell wall. Here
Jeske et al. show that Planctomycetes do possess a typical PG cell wall and that
their cellular architecture resembles that of Gram-negative bacteria.
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Affiliation(s)
- Olga Jeske
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Margarete Schüler
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Peter Schumann
- Department of Microbiology, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Alexander Schneider
- Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Christian Boedeker
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Mareike Jogler
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Daniel Bollschweiler
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Manfred Rohde
- Research Group Molecular Mechanisms of Streptococci, Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, Braunschweig 38124, Germany
| | - Christoph Mayer
- Department of Microbiology and Biotechnology, University of Tübingen, Auf der Morgenstelle 28, Tübingen 72076, Germany
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18, Martinsried 82152, Germany
| | - Stefan Spring
- Department of Microbiology, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
| | - Christian Jogler
- Independent Junior Research Group Microbial Cell Biology and Genetics, Leibniz Institute-DSMZ, Inhoffenstraße 7b, Braunschweig 38124, Germany
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