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Bai L, Paek J, Shin Y, Kim H, Kim SH, Shin JH, Kook JK, Chang YH. Description of an anaerobic actinobacterium, Kribbibacterium absianum gen. nov., sp. nov., a new member of the novel family Kribbibacteriaceae fam. nov., and reclassification of the genera Granulimonas and Leptogranulimonas. Int J Syst Evol Microbiol 2024; 74. [PMID: 38728210 DOI: 10.1099/ijsem.0.006382] [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: 05/12/2024] Open
Abstract
Two rod-shaped, obligate anaerobic, Gram-stain-positive bacteria isolated from the pig faeces were designated YH-ols2216 and YH-ols2217T. Analysis of 16S rRNA gene sequences revealed that these isolates were most related to the members of the family Atopobiaceae, within the order Coriobacteriales, and Granulimonas faecalis KCTC 25474T with 92.0 and 92.5% similarities, respectively. The 16S rRNA gene sequence similarity within isolates was 99.9 %; and those between isolates YH-ols2216 and YH-ols2217T, and Atopobium minutum DSM 20586T, the type species of the type genus Atopobium within the family Atopobiaceae, were 88.5 and 88.7 %, respectively. Those between isolates and Coriobacterium glomerans PW2T, the type species of the type genus Coriobacterium within the family Coriobacteriaceae, were 88.7 and 89.1 %, respectively. The multi-locus sequence tree revealed that the isolates, alongside the genera Granulimonas and Leptogranulimonas, formed a distinct cluster between the families Atopobiaceae and Coriobacteriaceae. The average nucleotide identities and digital DNA-DNA hybridization values for the isolates and their most closely related strains ranged from 67.7 to 76.2 % and from 18.4 to 23.3 %, respectively. The main cellular fatty acids of the isolates were C18 : 0 DMA, C18 : 1 ω9c, C18 : 0 12OH, C18 : 0, and C16 : 0. The cell wall contained the peptidoglycan meso-diaminopimelic acid. Lactate was the main end-product of the isolates. The major polar lipids of isolate YH-ols2217T were aminophospholipid, aminolipids, and lipids. Menaquinones were not identified in the cells of the isolates. The DNA G+C contents of isolates YH-ols2216 and YH-ols2217T were 67.5 and 67.6 mol%, respectively. Considering these chemotaxonomic, phenotypic, and phylogenetic properties, Kribbibacteriaceae fam. nov. is proposed within the order Coriobacteriales. YH-ols2216 (=KCTC 25708=NBRC 116429) and YH-ols2217T (=KCTC 25709T=NBRC 116430T) represent a novel taxon within this new family and the name Kribbibacterium absianum gen. nov., sp. nov. is proposed. In addition, the genera Granulimonas and Leptogranulimonas are transferred to the family Kribbibacteriaceae fam. nov.
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Affiliation(s)
- Lu Bai
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jayoung Paek
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Yeseul Shin
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hongik Kim
- Vitabio, Inc., Daejeon, Republic of Korea
| | - Si Hyun Kim
- Department of Biomedical Laboratory Science, Inje University, Gimhae, Republic of Korea
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Inje University College of Medicine, Busan, Republic of Korea
| | - Joong-Ki Kook
- Korean Collection for Oral Microbiology and Department of Oral Biochemistry, School of Dentistry, Chosun University, Gwangju, Republic of Korea
| | - Young-Hyo Chang
- ABS Research Support Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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Frias H, Murga Valderrama NL, Flores GJ, Cornejo VG, Del Solar JC, Romani AC, Bardales W, Segura GT, Polveiro RC, Vieira DDS, Lopez Lapa RM, Maicelo Quintana JL. An analysis of the cecum microbiome of three breeds of the guinea pig: Andina, Inti, and Peru. Res Vet Sci 2023; 161:50-61. [PMID: 37321011 DOI: 10.1016/j.rvsc.2023.06.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/17/2023]
Abstract
This study investigated the effect of host genetics on the structure and composition of the cecum microbiota of three breeds of guinea pigs: Andina, Inti, and Peru. Fifteen guinea pigs were distributed into three groups according to their breed: Andina (5), Inti (5), and Peru (5). We discovered that four main phyla were shared between the three breeds: Bacteroidota, Firmicutes, Spirochaetota, and Synergistota. Although there were no significant differences in the alpha and beta diversity analysis, we found that the Linear discriminant analysis effect size and the heat tree analysis showed significant differences between the abundance of several taxa present in the cecum microbiome of the three breeds. These results suggest that host genetics could be a factor in the structure and composition of the guinea pig cecum microbiome. In addition, we found unique genera for each breed that have fermentation capacity and, therefore can be analyzed in further studies to determine if there is a functional relationship between them and the breed and its industrial profile.
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Affiliation(s)
- Hugo Frias
- Academic Department of Zootechnics, Faculty of Zootechnical Engineering, Agribusiness and Biotechnology, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Nilton Luis Murga Valderrama
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Gary J Flores
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Victor G Cornejo
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Jakson Ch Del Solar
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Ana C Romani
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - William Bardales
- Laboratory of Infectious and Parasitic Diseases, Livestock and Biotechnology Research Institute, Faculty of Zootechnical Engineering, Agribusiness, and Biotechnology, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - G T Segura
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
| | - Richard C Polveiro
- Laboratory of Bacterial Diseases, Sector of Preventive Veterinary Medicine and Public Health, Department of Veterinary, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Dielson da S Vieira
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Rainer M Lopez Lapa
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru; Department of Public Health, Faculty of Health Sciences, National University Toribio Rodríguez de Mendoza de Amazonas, Chachapoyas, Peru.
| | - Jorge Luis Maicelo Quintana
- Livestock and Biotechnology Research Institute, National University Toribio Rodríguez de Mendoza, Amazonas, Peru
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Liu Y, Angelov A, Feiler W, Baudrexl M, Zverlov V, Liebl W, Vanderhaeghen S. Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:121. [PMID: 36371193 PMCID: PMC9655821 DOI: 10.1186/s13068-022-02216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited. RESULTS In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-L-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan). CONCLUSIONS We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.
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Affiliation(s)
- Yajing Liu
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: Chair of Chemistry of Biogenic Resources, Technical University of Munich, Schulgasse 16, 94315 Straubing, Germany
| | - Angel Angelov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076 Tübingen, Germany
| | - Werner Feiler
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Vladimir Zverlov
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
| | - Sonja Vanderhaeghen
- Chair of Microbiology, Technical University of Munich, Emil-Ramann-Straβe 4, 85354 Freising-Weihenstephan, Germany
- Present Address: IMGM Laboratories, Lochhamer Straße 29a, 82152 Planegg, Germany
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Kabaivanova L, Hubenov V, Dimitrova L, Simeonov I, Wang H, Petrova P. Archaeal and Bacterial Content in a Two-Stage Anaerobic System for Efficient Energy Production from Agricultural Wastes. Molecules 2022; 27:1512. [PMID: 35268611 PMCID: PMC8911581 DOI: 10.3390/molecules27051512] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/22/2022] Open
Abstract
Anaerobic digestion (AD) is a microbially-driven process enabling energy production. Microorganisms are the core of anaerobic digesters and play an important role in the succession of hydrolysis, acidogenesis, acetogenesis, and methanogenesis processes. The diversity of participating microbial communities can provide new information on digester performance for biomass valorization and biofuel production. In this study anaerobic systems were used, operating under mesophilic conditions that realized biodegradation processes of waste wheat straw pretreated with NaOH-a renewable source for hydrogen and methane production. These processes could be managed and optimized for hydrogen and methane separately but combining them in a two-stage system can lead to higher yields and a positive energy balance. The aim of the study was to depict a process of biohydrogen production from lignocellulosic waste followed by a second one leading to the production of biomethane. Archaeal and bacterial consortia in a two-stage system operating with wheat straw were identified for the first time and the role of the most important representatives was elucidated. The mixed cultures were identified by the molecular-biological methods of metagenomics. The results showed that biohydrogen generation is most probably due to the presence of Proteiniphilum saccharofermentans, which was 28.2% to 45.4% of the microbial community in the first and the second bioreactor, respectively. Archaeal representatives belonging to Methanobacterium formicicum (0.71% of the community), Methanosarcina spelaei (0.03%), Methanothrix soehngenii (0.012%), and Methanobacterium beijingense (0.01%) were proven in the methane-generating reactor. The correlation between substrate degradation and biogas accumulation was calculated, together with the profile of fatty acids as intermediates produced during the processes. The hydrogen concentration in the biogas reached 14.43%, and the Methane concentration was 69%. Calculations of the energy yield during the two-stage process showed 1195.89 kWh·t-1 compared to a 361.62 kWh·t-1 cumulative yield of energy carrier for a one-stage process.
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Affiliation(s)
- Lyudmila Kabaivanova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Venelin Hubenov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Lyudmila Dimitrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Ivan Simeonov
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
| | - Haoping Wang
- French-Chinese Laboratory LaFCAS, School of Automation, Nanjing University of Science and Technology, Nanjing 210094, China;
| | - Penka Petrova
- Institute of Microbiology, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (V.H.); (L.D.); (I.S.)
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Impact of Granular Activated Carbon on Anaerobic Process and Microbial Community Structure during Mesophilic and Thermophilic Anaerobic Digestion of Chicken Manure. SUSTAINABILITY 2022. [DOI: 10.3390/su14010447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this work, the impact of granular activated carbon (GAC) on the mesophilic and thermophilic anaerobic digestion of chicken manure and the structure of microbial communities was investigated. These results demonstrated that GAC supplementation effectively enhanced the consumption of produced organic acids in the mesophilic and thermophilic batch tests, accompanied by faster biomethane production in the presence of GAC than from reactors without GAC. However, since the free ammonia level was 3–6 times higher in the thermophilic reactors, this led to the instability of the anaerobic digestion process of the nitrogen-rich substrate at thermophilic temperatures. Bacteroidia and Clostridia were the two main bacterial classes in the mesophilic reactors, whereas the class Clostridia had a competitive advantage over other groups in the thermophilic systems. The archaeal communities in the mesophilic reactors were mainly represented by representatives of the genera Methanosarcina, Methanobacterium, and Methanotrix, whereas the archaeal communities in the thermophilic reactors were mainly represented by members of the genera Methanosarcina, Methanoculleus, and Methanothermobacter. New data obtained in this research will help control and manage biogas reactors in the presence of GAC at different temperatures.
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Rettenmaier R, Thieme N, Streubel J, Di Bello L, Kowollik ML, Huang L, Maus I, Klingl A, Liebl W, Zverlov VV. Variimorphobacter saccharofermentans gen. nov., sp. nov., a new member of the family Lachnospiraceae, isolated from a maize-fed biogas fermenter. Int J Syst Evol Microbiol 2021; 71. [PMID: 34731077 DOI: 10.1099/ijsem.0.005044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MD1T is an anaerobic, Gram-stain-negative bacterium isolated from a lab-scale biogas fermenter fed with maize silage. It has a rod-shaped morphology with peritrichously arranged appendages and forms long chains of cells and coccoid structures. The colonies of MD1T were white, circular, slightly convex and had a smooth rim. The isolate is mesophilic, displaying growth between 25 and 45 °C with an optimum at 40 °C. It grew at pH values of pH 6.7-8.2 (optimum, pH 7.1) and tolerated the addition of up to 1.5% (w/v) NaCl to the medium. The main cellular fatty acids of MD1T are C14:0 DMA and C16:0. Strain MD1T fermented xylose, arabinose, glucose, galactose, cellobiose, maltose, maltodextrin10, lactose starch, and xylan, producing mainly 2-propanol and acetic acid. The genome of the organism has a total length of 4163427 bp with a G+C content of 38.5 mol%. The two closest relatives to MD1T are Mobilitalea sibirica P3M-3T and Anaerotaenia torta FH052T with 96.44 or 95.8 % 16S rRNA gene sequence similarity and POCP values of 46.58 and 50.58%, respectively. As MD1T showed saccharolytic and xylanolytic properties, it may play an important role in the biogas fermentation process. Closely related variants of MD1T were also abundant in microbial communities involved in methanogenic fermentation. Based on morphological, phylogenetic and genomic data, the isolated strain can be considered as representing a novel genus in the family Lachnospiraceae, for which the name Variimorphobacter saccharofermentans gen. nov., sp. nov. (type strain MD1T=DSM 110715T=JCM 39125T) is proposed.
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Affiliation(s)
- Regina Rettenmaier
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Nils Thieme
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Johanna Streubel
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Luca Di Bello
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Marie-Louise Kowollik
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Liren Huang
- Faculty of Technology, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Irena Maus
- Center for Biotechnology (CeBiTec), Genome Research of Industrial Microorganisms, Bielefeld University, Universitätsstr. 27, 33615 Bielefeld, Germany
| | - Andreas Klingl
- Ludwig-Maximilians-Universität Munich, Plant Development & Electron Microscopy, Biocenter LMU Munich, Großhadernerstr. 2-4, 82152 Planegg-Martinsried, Germany
| | - Wolfgang Liebl
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany
| | - Vladimir V Zverlov
- Technical University of Munich, Chair of Microbiology, Emil-Ramann-Str. 4, 85354 Freising, Germany.,Institute of Molecular Genetics, National Research Centre 'Kurchatov Institute', Kurchatov Sq 2, 123182 Moscow, Russia
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