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Teullet S, Tilak MK, Magdeleine A, Schaub R, Weyer NM, Panaino W, Fuller A, Loughry WJ, Avenant NL, de Thoisy B, Borrel G, Delsuc F. Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals. mSystems 2023; 8:e0038823. [PMID: 37650612 PMCID: PMC10654083 DOI: 10.1128/msystems.00388-23] [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: 04/20/2023] [Accepted: 06/19/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.
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Affiliation(s)
- Sophie Teullet
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Marie-Ka Tilak
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Amandine Magdeleine
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Roxane Schaub
- CIC AG/Inserm 1424, Centre Hospitalier de Cayenne Andrée Rosemon, Cayenne, French Guiana, France
- Tropical Biome and immunopathology, Université de Guyane, Labex CEBA, DFR Santé, Cayenne, French Guiana, France
| | - Nora M. Weyer
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - Wendy Panaino
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
- Centre for African Ecology, School of Animals, Plant, and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrea Fuller
- Brain Function Research Group, School of Physiology, University of the Witwatersrand, Johannesburg, South Africa
| | - W. J. Loughry
- Department of Biology, Valdosta State University, Valdosta, Georgia, USA
| | - Nico L. Avenant
- National Museum and Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Benoit de Thoisy
- Institut Pasteur de la Guyane, Cayenne, French Guiana, France
- Kwata NGO, Cayenne, French Guiana, France
| | - Guillaume Borrel
- Evolutionary Biology of the Microbial Cell, Institut Pasteur, Université Paris Cité, Paris, France
| | - Frédéric Delsuc
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, CNRS, IRD, Montpellier, France
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2
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Thakur D, Chauhan A, Jhilta P, Kaushal R, Dipta B. Microbial chitinases and their relevance in various industries. Folia Microbiol (Praha) 2023; 68:29-53. [PMID: 35972681 DOI: 10.1007/s12223-022-00999-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/31/2022] [Indexed: 01/09/2023]
Abstract
Chitin, the second most abundant biopolymer on earth after cellulose, is composed of β-1,4-N-acetylglucosamine (GlcNAc) units. It is widely distributed in nature, especially as a structural polysaccharide in the cell walls of fungi, the exoskeletons of crustaceans, insects, and nematodes. However, the principal commercial source of chitin is the shells of marine or freshwater invertebrates. Microbial chitinases are largely responsible for chitin breakdown in nature, and they play an important role in the ecosystem's carbon and nitrogen balance. Several microbial chitinases have been characterized and are gaining prominence for their applications in various sectors. The current review focuses on chitinases of microbial origin, their diversity, and their characteristics. The applications of chitinases in several industries such as agriculture, food, the environment, and pharmaceutical sectors are also highlighted.
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Affiliation(s)
- Deepali Thakur
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Anjali Chauhan
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Prakriti Jhilta
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Rajesh Kaushal
- Dr Yashwant Singh Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, Himachal Pradesh, India
| | - Bhawna Dipta
- ICAR-Central Potato Research Institute, Shimla, 171001, Himachal Pradesh, India.
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3
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Dohnálek J, Dušková J, Tishchenko G, Kolenko P, Skálová T, Novák P, Fejfarová K, Šimůnek J. Chitinase Chit62J4 Essential for Chitin Processing by Human Microbiome Bacterium Clostridium paraputrificum J4. Molecules 2021; 26:molecules26195978. [PMID: 34641521 PMCID: PMC8512545 DOI: 10.3390/molecules26195978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Commensal bacterium Clostridium paraputrificum J4 produces several extracellular chitinolytic enzymes including a 62 kDa chitinase Chit62J4 active toward 4-nitrophenyl N,N'-diacetyl-β-d-chitobioside (pNGG). We characterized the crude enzyme from bacterial culture fluid, recombinant enzyme rChit62J4, and its catalytic domain rChit62J4cat. This major chitinase, securing nutrition of the bacterium in the human intestinal tract when supplied with chitin, has a pH optimum of 5.5 and processes pNGG with Km = 0.24 mM and kcat = 30.0 s-1. Sequence comparison of the amino acid sequence of Chit62J4, determined during bacterial genome sequencing, characterizes the enzyme as a family 18 glycosyl hydrolase with a four-domain structure. The catalytic domain has the typical TIM barrel structure and the accessory domains-2x Fn3/Big3 and a carbohydrate binding module-that likely supports enzyme activity on chitin fibers. The catalytic domain is highly homologous to a single-domain chitinase of Bacillus cereus NCTU2. However, the catalytic profiles significantly differ between the two enzymes despite almost identical catalytic sites. The shift of pI and pH optimum of the commensal enzyme toward acidic values compared to the soil bacterium is the likely environmental adaptation that provides C. paraputrificum J4 a competitive advantage over other commensal bacteria.
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Affiliation(s)
- Jan Dohnálek
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
- Correspondence: ; Tel.: +420-325-873-758; Fax: +420-325-873-710
| | - Jarmila Dušková
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Galina Tishchenko
- Department of Structural Analysis of Biomacromolecules, Institute of Macromolecular Chemistry of the Czech Academy of Sciences, v. v. i., Heyrovsky Sq. 2, 162 06 Prague, Czech Republic;
| | - Petr Kolenko
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Tereza Skálová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Petr Novák
- Laboratory of Structural Biology and Cell Signaling, Institute of Microbiology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic;
| | - Karla Fejfarová
- Laboratory of Structure and Function of Biomolecules, Institute of Biotechnology of the Czech Academy of Sciences, v. v. i., Biocev, Průmyslová 595, 252 50 Vestec, Czech Republic; (J.D.); (P.K.); (T.S.); (K.F.)
| | - Jiří Šimůnek
- Laboratory of Anaerobic Microbiology, Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, v. v. i., Vídeňská 1083, 142 00 Prague, Czech Republic;
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4
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Recent advances in the bioprospection and applications of chitinolytic bacteria for valorization of waste chitin. Arch Microbiol 2021; 203:1953-1969. [PMID: 33710379 DOI: 10.1007/s00203-021-02234-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 01/12/2021] [Accepted: 02/11/2021] [Indexed: 10/21/2022]
Abstract
One of the most abundant natural polymers on earth, chitin is a fibrous and structural polysaccharide, composed of N-acetyl-D-glucosamine. The biopolymer is the major structural constituent of fungi, arthropods, mollusks, nematodes, and some algae. The biodegradation of chitin is largely manifested by chitinolytic enzyme secreting organisms including bacteria, insects, and plants. Among them, bacterial chitinases represent the most promising, inexpensive, and sustainable source of proteins that can be employed for industrial-scale applications. To this end, the presented review comes at a timely moment to highlight the major sources of chitinolytic bacteria. It also discusses the potential pros and cons of prospecting bacterial chitinases that can be easily manipulated through genetic engineering. Additionally, we have elaborated the recent applications of the chitin thereby branding chitinases as potential candidates for biorefinery and biomedical research for eco-friendly and sustainable management of chitin waste in the environment.
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Denison ER, Rhodes RG, McLellan WA, Pabst DA, Erwin PM. Host phylogeny and life history stage shape the gut microbiome in dwarf (Kogia sima) and pygmy (Kogia breviceps) sperm whales. Sci Rep 2020; 10:15162. [PMID: 32938948 PMCID: PMC7495435 DOI: 10.1038/s41598-020-72032-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/20/2020] [Indexed: 01/05/2023] Open
Abstract
Gut microbiomes perform crucial roles in host health and development, but few studies have explored cetacean microbiomes especially deep divers. We characterized the gut microbiomes of stranded dwarf (Kogia sima) and pygmy (K. breviceps) sperm whales to examine the effects of phylogeny and life stage on microbiome composition and diversity. 16S rRNA gene sequence analysis revealed diverse gut communities (averaging 674 OTUs) dominated by a few symbiont taxa (25 OTUs accounted for 64% of total relative abundance). Both phylogeny and life stage shaped community composition and diversity, with species-specific microbiome differences present early in life. Further analysis showed evidence of microbiome convergence with host maturity, albeit through different processes: symbiont 'accumulation' in K. sima and 'winnowing' in K. breviceps, indicating different methods of community assembly during host development. Furthermore, culture-based analyses yielded 116 pure cultures matching 25 OTUs, including one isolate positive for chitin utilization. Our findings indicate that kogiid gut microbiomes are highly diverse and species-specific, undergo significant shifts with host development, and can be cultivated on specialized media under anaerobic conditions. These results enhance our understanding of the kogiid gut microbiome and may provide useful information for symbiont assessment in host health.
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Affiliation(s)
- Elizabeth R Denison
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Ryan G Rhodes
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - William A McLellan
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - D Ann Pabst
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA
| | - Patrick M Erwin
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, 28409, USA.
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Genome Sequence of Clostridium paraputrificum 373-A1 Isolated in Chile from a Patient Infected with Clostridium difficile. GENOME ANNOUNCEMENTS 2016; 4:4/6/e01178-16. [PMID: 27811092 PMCID: PMC5095462 DOI: 10.1128/genomea.01178-16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
ABSTRACT
Clostridium paraputrificum
is a gut microbiota member reported in several cases of bacteremia and coinfections. So far, only one genome sequence of a
C. paraputrificum
(AGR2156) isolate is available. Here, we present the draft genome of
C. paraputrificum
strain 373-A1, isolated from stools from a patient with
C. difficile
infection.
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7
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Delport TC, Power ML, Harcourt RG, Webster KN, Tetu SG. Colony Location and Captivity Influence the Gut Microbial Community Composition of the Australian Sea Lion (Neophoca cinerea). Appl Environ Microbiol 2016; 82:3440-3449. [PMID: 27037116 PMCID: PMC4959163 DOI: 10.1128/aem.00192-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/19/2016] [Indexed: 02/01/2023] Open
Abstract
UNLABELLED Gut microbiota play an important role in maintenance of mammalian metabolism and immune system regulation, and disturbances to this community can have adverse impacts on animal health. To better understand the composition of gut microbiota in marine mammals, fecal bacterial communities of the Australian sea lion (Neophoca cinerea), an endangered pinniped with localized distribution, were examined. A comparison of samples from individuals across 11 wild colonies in South and Western Australia and three Australian captive populations showed five dominant bacterial phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria The phylum Firmicutes was dominant in both wild (76.4% ± 4.73%) and captive animals (61.4% ± 10.8%), while Proteobacteria contributed more to captive (29.3% ± 11.5%) than to wild (10.6% ± 3.43%) fecal communities. Qualitative differences were observed between fecal communities from wild and captive animals based on principal-coordinate analysis. SIMPER (similarity percentage procedure) analyses indicated that operational taxonomic units (OTU) from the bacterial families Clostridiaceae and Ruminococcaceae were more abundant in wild than in captive animals and contributed most to the average dissimilarity between groups (SIMPER contributions of 19.1% and 10.9%, respectively). Differences in the biological environment, the foraging site fidelity, and anthropogenic impacts may provide various opportunities for unique microbial establishment in Australian sea lions. As anthropogenic disturbances to marine mammals are likely to increase, understanding the potential for such disturbances to impact microbial community compositions and subsequently affect animal health will be beneficial for management of these vulnerable species. IMPORTANCE The Australian sea lion is an endangered species for which there is currently little information regarding disease and microbial ecology. In this work, we present an in-depth study of the fecal microbiota of a large number of Australian sea lions from geographically diverse wild and captive populations. Colony location and captivity were found to influence the gut microbial community compositions of these animals. Our findings significantly extend the baseline knowledge of marine mammal gut microbiome composition and variability.
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Affiliation(s)
- Tiffany C Delport
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Michelle L Power
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Robert G Harcourt
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Koa N Webster
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, New South Wales, Australia
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8
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O'Hara PJ, Klieve AV, Murray PJ, Maguire AJ, Ouwerkerk D, Harper K. Effect of time and diet change on the bacterial community structure throughout the gastrointestinal tract and in faeces of the northern brown bandicoot, Isoodon macrourus. AUST J ZOOL 2016. [DOI: 10.1071/zo15078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A significant gap, in not only peramelid nutritional physiology but marsupial nutrition as a whole, is the lack of information relating to microorganisms of the gastrointestinal tract. This research is a preliminary investigation that will provide a baseline for comparisons among peramelids. The high degree of 16S rRNA gene clones identified in this research that are closely related to culturable bacteria suggests that additional research will enable a more complete description of the gastrointestinal bacteria of I. macrourus. Most identifiable clones belonged to Clostridium and Ruminococcus. This research has confirmed that the hindgut of I. macrourus, the caecum, proximal colon and distal colon, are the main sites for microbial activity.
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9
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Lu Y, Zhao H, Zhang C, Xing XH. Insights into the global regulation of anaerobic metabolism for improved biohydrogen production. BIORESOURCE TECHNOLOGY 2016; 200:35-41. [PMID: 26476162 DOI: 10.1016/j.biortech.2015.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 10/02/2015] [Accepted: 10/06/2015] [Indexed: 06/05/2023]
Abstract
To improve the biohydrogen yield in bacterial dark fermentation, a new approach of global anaerobic regulation was introduced. Two cellular global regulators FNR and NarP were overexpressed in two model organisms: facultatively anaerobic Enterobacter aerogenes (Ea) and strictly anaerobic Clostridium paraputrificum (Cp). The overexpression of FNR and NarP greatly altered anaerobic metabolism and increased the hydrogen yield by 40%. Metabolic analysis showed that the global regulation caused more reducing environment inside the cell. To get a thorough understanding of the global metabolic regulation, more genes (fdhF, fhlA, ppk, Cb-fdh1, and Sc-fdh1) were overexpressed in different Ea and Cp mutants. For the first time, it demonstrated that there were approximately linear relationships between the relative change of hydrogen yield and the relative change of NADH yield or ATP yield. It implied that cellular reducing power and energy level played vital roles in the biohydrogen production.
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Affiliation(s)
- Yuan Lu
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Hongxin Zhao
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China; Zhejiang Province Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China; College of Chemistry and Life Sciences, Shenyang Normal University, Shenyang 110034, China
| | - Chong Zhang
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xin-Hui Xing
- Key Lab of Industrial Biocatalysis of Ministry of Education (Tsinghua University), China; Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
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10
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Simůnek J, Koppová I, Tiščenko G, Dohnálek J, Dušková J. Excretome of the chitinolytic bacterium Clostridium paraputrificum J4. Folia Microbiol (Praha) 2012; 57:335-9. [PMID: 22528309 DOI: 10.1007/s12223-012-0137-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2011] [Accepted: 03/04/2012] [Indexed: 10/28/2022]
Abstract
A strictly anaerobic mesophilic chitinolytic bacterial strain identified as Clostridium paraputrificum J4 was isolated from human feces. In response to various types of growth substrates, the bacterium produced an array of chitinolytic enzymes representing significant components of the J4 strain secretome. The excreted active proteins were characterized by estimating the enzymatic activities of endochitinase, exochitinase, and N-acetylglucosaminidase induced by cultivation in medium M-10 with colloidal chitin. The enzyme activities produced by J4 strain cultivated in medium M-10 with glucose were significantly lower. The spectrum of extracellularly excreted proteins was separated by SDS-PAGE. The chitinase variability was confirmed on zymograms of renatured SDS-PAGE. The enzymes were visualized under ultraviolet light by using 4-methylumbelliferyl derivatives of N-acetyl-β-D: -glucosaminide, N,N´-diacetyl-β-D: -chitobiose, or N,N´,N˝-triacetyl-β-D: -chitotriose for β-N-acetylglucosaminidase, chitobiosidase, or endochitinase activities, respectively. Protein components of the secretome were separated by 2D-PAGE analysis. The distinct protein bands were excised, isolated, and subsequently characterized by using MALDI-TOF/TOF tandem mass spectrometry. The final identification was performed according to sequence homology by database searching.
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Affiliation(s)
- Jiří Simůnek
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic.
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Muzzarelli RA, Boudrant J, Meyer D, Manno N, DeMarchis M, Paoletti MG. Current views on fungal chitin/chitosan, human chitinases, food preservation, glucans, pectins and inulin: A tribute to Henri Braconnot, precursor of the carbohydrate polymers science, on the chitin bicentennial. Carbohydr Polym 2012. [DOI: 10.1016/j.carbpol.2011.09.063] [Citation(s) in RCA: 524] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Tishchenko G, Simůnek J, Bartoňová H, Dušková J, Dohnálek J, Ponomareva E, Tennikova T. Sample preparation in separation of the extracellular chitinolytic enzymes of the human intestinal bacterium Clostridium paraputrificum J4 from the culture fluids. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:2175-8. [PMID: 21703948 DOI: 10.1016/j.jchromb.2011.05.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 05/05/2011] [Accepted: 05/24/2011] [Indexed: 10/18/2022]
Abstract
Membrane ultrafiltration (UF) was used in sample preparation of the culture fluids of the human intestinal bacterium Clostridium paraputrificum strain J4 containing seven extracellular chitinolytic isoenzymes (38-90 kDa). The subsequent filtration of the bacteria-free supernatants was carried out through Millipore membranes with cut-off 100 and 30 kDa for separation of undigested components of the culture medium and bacterial metabolites with molecular weight higher and lower than that of the target enzymes. The chitinolytic enzymes, which were the minor components in the culture fluids, were concentrated at UF as well. The aim of the research consisted in evaluation of the effect of component composition of bacteria-free supernatants and the chemical nature of membrane active layer on partial fractionation of the chitinolytic enzymes, their recovery in retentates and purification degree. On the basis of the obtained experimental results, the sample preparation procedure of the culture fluids of C. paraputrificum J4 was established to be used further in chromatographic separations of the chitinolytic enzymes.
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Affiliation(s)
- Galina Tishchenko
- Institute of Macromolecular Chemistry AS CR, vvi, Prague, Czech Republic.
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Tishchenko G, Koppová I, Simůnek J, Dohnálek J. Extracellular complex of chitinolytic enzymes of Clostridium paraputrificum strain J4 separated by membrane ultrafiltration. Folia Microbiol (Praha) 2010; 55:386-9. [PMID: 20680578 DOI: 10.1007/s12223-010-0065-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Revised: 04/14/2010] [Indexed: 11/28/2022]
Abstract
Membrane diafiltration was used for separation of the extracellular complex of chitinolytic enzymes of C. paraputrificum J4 free from contaminants with molar mass higher than 100 kDa and lower than 30 kDa. The enzyme complex containing beta-N-acetylglucosaminidase (NAGase) and six endochitinases was concentrated on a membrane with cut-off 30 kDa. In this retentate, the NAGase/endochitinase specific activity was 13.5/6.5-times higher than in the initial culture filtrate. The proportion (in%) of endochitinases: 23 (90 kDa), 42 (86 kDa), 8 (72 kDa), 16 (68 kDa) and 8 (60 kDa) was calculated from their peak areas (determined by densitometry) in images of zymograms. NAGase (38 kDa) was less active and stable at pH lower than 4 and higher than 8 but it was more temperature-stable than endochitinases, especially at 40-60 degrees C. In contrast to endochitinases, the pH optimum of NAGase activity was shifted by ca. 0.7 pH units to the alkaline region. Extracellular NAGase together with six endochitinases secreted by C. paraputrificum J4 were separated by membrane diafiltration and characterized by molar mass, stability and activity in dependence on pH and temperature. The knowledge of composition of chitinolytic enzymes, their pH and temperature stability is useful for optimization of the separation process.
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Affiliation(s)
- G Tishchenko
- Institute of Macromolecular Chemistry AS CR, v.v.i., 162 06, Prague 6, Czech Republic
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14
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Simůnek J, Tishchenko G, Koppová I. Chitinolytic activities of Clostridium sp. JM2 isolated from stool of human administered per orally by chitosan. Folia Microbiol (Praha) 2008; 53:249-54. [PMID: 18661303 DOI: 10.1007/s12223-008-0037-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 01/17/2008] [Indexed: 11/28/2022]
Abstract
The novel chitinolytic bacterium Clostridium beijerinckii strain JM2 was isolated from the stool of healthy volunteers supplied daily per orally with 3 g of chitosan. The bacterium grown on colloidal chitin produced a complete array of chitinolytic enzymes. Significant activities of endochitinase, exochitinase and chitosanase were excreted into the medium (301, 282 and 268 nkat/microg protein, respectively). The high cellular activity of N-acetyl-beta-glucosaminidase (NAGase) and chitosanase were detected (732.4 and 154 nkat/microg protein, respectively). NAGase activity represented the main activity associated with the cellular fraction. The activities of both enzymes tested increased from 20 to 50 degrees C; the optimum reaction temperature estimated being 50 degrees C. Endochitinase as well as NAGase showed an activity in the pH interval of 4.0-8.0; the optimum pH values were 6.5 and 6.0, respectively. The extracellular endochitinase complex consisted of six isoenzymes with molar mass of 32-76 kDa; in the cellular fraction five bands with molar mass of 45-86 kDa were detected. Exochitinase activity was demonstrated in the form of three bands (with molar mass of 30-57 kDa), NAGase activity displayed one band of 45 kDa.
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Affiliation(s)
- J Simůnek
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia.
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15
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Simůnek J, Tishchenko G, Hodrová B, Bartonová H. Effect of chitosan on the growth of human colonic bacteria. Folia Microbiol (Praha) 2006; 51:306-8. [PMID: 17007432 DOI: 10.1007/bf02931820] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Growth of 6 bacterial strains representing dominant members of the human colonic microflora was measured in the presence of 0.025, 0.05 and 0.5 % chitosan (from shrimp shells, with a 97 % final degree of deacetylation). The effect of chitosan was variable and dependent on bacterial species. The most susceptible to chitosan were bacteria belonging to genera Bacteroides and Clostridium (91-97% growth inhibition). On the other hand, Roseburia sp., Eubacterium sp. and Faecalibacterium sp. were more resistant (63-83 % inhibition of growth). Chitosan can thus be considered as one of the means for influencing the bacterial population in the human colon.
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Affiliation(s)
- J Simůnek
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Prague, Czechia.
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16
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Ouwerkerk D, Klieve AV, Forster RJ, Templeton JM, Maguire AJ. Characterization of culturable anaerobic bacteria from the forestomach of an eastern grey kangaroo, Macropus giganteus. Lett Appl Microbiol 2005; 41:327-33. [PMID: 16162139 DOI: 10.1111/j.1472-765x.2005.01774.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIM To determine the culturable biodiversity of anaerobic bacteria isolated from the forestomach contents of an eastern grey kangaroo, Macropus giganteus, using phenotypic characterization and 16S rDNA sequence analysis. METHODS AND RESULTS Bacteria from forestomach contents of an eastern grey kangaroo were isolated using anaerobic media containing milled curly Mitchell grass (Astrebla lappacea). DNA was extracted and the 16S rDNA sequenced for phylogenetic analysis. Forty bacterial isolates were obtained and placed in 17 groups based on phenotypic characteristics and restriction enzyme digestion of 16S rDNA PCR products. DNA sequencing revealed that the 17 groups comprised five known species (Clostridium butyricum, Streptococcus bovis, Clostridium sporogenes, Clostridium paraputrificum and Enterococcus avium) and 12 groups apparently representing new species, all within the phylum Firmicutes. CONCLUSIONS Foregut contents from Australian macropod marsupials contain a microbial ecosystem with a novel bacterial biodiversity comprising a high percentage of previously unrecognized species. SIGNIFICANCE AND IMPACT OF THE STUDY This study adds to knowledge of Australia's unique biodiversity, which may provide a future bioresource of genetic information and bacterial species of benefit to agriculture.
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MESH Headings
- Animals
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/growth & development
- Bacteria, Anaerobic/isolation & purification
- Culture Media
- DNA, Bacterial/analysis
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/analysis
- Macropodidae/microbiology
- Molecular Sequence Data
- Phenotype
- Phylogeny
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- Restriction Mapping
- Sequence Analysis, DNA
- Stomach/microbiology
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Affiliation(s)
- D Ouwerkerk
- Animal Science, Department of Primary Industries and Fisheries (DPI&F), Yeerongpilly, Queensland, Australia
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Kopecný J, Hajer J, Mrázek J. Detection of cellulolytic bacteria from the human colon. Folia Microbiol (Praha) 2005; 49:175-7. [PMID: 15227792 DOI: 10.1007/bf02931396] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The main representatives of bacteria in the human colon were investigated by specific PCR and denaturing gradient gel electrophoresis (DGGE). Prevalent in both cases were species of Bifidobacterium, Clostridium, Bacteroides, Faecalibacterium and Eubacterium. Simultaneously, cellulolytic bacteria were isolated from the human feces. The largest proportion was represented by ruminococcus-like isolates. Their presence was confirmed both by PCR and DGGE methods; the latter one was able to give more comprehensive data about the composition of bacterial population in the human colon chyme.
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Affiliation(s)
- J Kopecný
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia.
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18
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Simůnek J, Tishchenko G, Rozhetsky K, Bartonová H, Kopecný J, Hodrová B. Chitinolytic enzymes fromClostridium aminovalericum: Activity screening and purification. Folia Microbiol (Praha) 2004; 49:194-8. [PMID: 15227797 DOI: 10.1007/bf02931401] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
A strain isolated from the feces of takin was identified as Clostridium aminovalericum. In response to various types of chitin used as growth substrates, the bacterium produced a complete array of chitinolytic enzymes: chitinase ('endochitinase'), exochitinase, beta-N-acetylglucosaminidase, chitosanase and chitin deacetylase. The highest activities of chitinase (536 pkat/mL) and exochitinase (747 pkat/mL) were induced by colloidal chitin. Fungal chitin also induced high levels of these enzymes (463 pkat/mL and 502 pkat/mL, respectively). Crab shell chitin was the best inducer of chitosanase activity (232 pkat/mL). The chitinolytic enzymes of this strain were separated from culture filtrate by ion-exchange chromatography on the carboxylic sorbent Polygran 27. At pH 4.5, some isoforms of the chitinolytic enzymes (30% of total enzyme activity) did not bind to Polygran 27. The enzymes were eluted under a stepwise pH gradient (pH 5-8) in 0.1 mol/L phosphate buffer. At merely acidic pH (4.5-5.5), the adsorbed enzymes were co-eluted. However, at pH close to neutral values, the peaks of highly purified isoforms of exochitinases and chitinases were isolated. The protein and enzyme recovery reached 90%.
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Affiliation(s)
- J Simůnek
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia.
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Cruz Camarillo R, Sánchez Pérez O, Rojas Avelizapa NG, Gómez Ramírez M, Rojas Avelizapa LI. Chitosanase activity in Bacillus thuringiensis. Folia Microbiol (Praha) 2004; 49:94-6. [PMID: 15114873 DOI: 10.1007/bf02931653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The ability to produce extracellular chitosanase (EC 3.2.1.132) was found by plate assays in 18 (23%) out of 77 crystalliferous strains of Bacillus thuringiensis. The best chitosanase producer was selected after the growth chosen in a liquid medium with colloidal chitosan as carbon source. Enzyme production was optimized (a 4-d incubation at 32 degrees C with shaking in a medium of pH 6.5 with 4% colloidal chitosan) and the enzyme was partially characterized. This is the first report on the chitosanase of B. thuringiensis.
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Affiliation(s)
- R Cruz Camarillo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politecnico National, México 11340, DF, México.
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Flieger M, Kantorová M, Prell A, Rezanka T, Votruba J. Biodegradable plastics from renewable sources. Folia Microbiol (Praha) 2003; 48:27-44. [PMID: 12744074 DOI: 10.1007/bf02931273] [Citation(s) in RCA: 217] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Plastic waste disposal is a huge ecotechnological problem and one of the approaches to solving this problem is the development of biodegradable plastics. This review summarizes data on their use, biodegradability, commercial reliability and production from renewable resources. Some commercially successful biodegradable plastics are based on chemical synthesis (i.e. polyglycolic acid, polylactic acid, polycaprolactone, and polyvinyl alcohol). Others are products of microbial fermentations (i.e. polyesters and neutral polysaccharides) or are prepared from chemically modified natural products (e.g., starch, cellulose, chitin or soy protein).
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Affiliation(s)
- M Flieger
- Institute of Microbiology, Academy of Sciences of the Czech Republic, 142 20 Prague, Czechia
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