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Xiao K, Abbt-Braun G, Pleitner R, Horn H. Effect of ciprofloxacin on the one-stage partial nitrification and anammox biofilm system: A multivariate analysis focusing on size-fractionated organic components. CHEMOSPHERE 2024; 355:141731. [PMID: 38494003 DOI: 10.1016/j.chemosphere.2024.141731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 02/13/2024] [Accepted: 03/14/2024] [Indexed: 03/19/2024]
Abstract
The impact of ciprofloxacin (CIP) in the partial nitrification and anammox biofilm system was investigated by multivariate analysis, focusing on size-fractionated organic components. The CIP dose of 10 μg/L did not inhibit the total nitrogen (TN) removal efficiency, even though the abundance of antibiotic resistant genes (ARGs) (i.e., qnrD, qnrB, qnrA, qnrS, and arcA) was elevated. However, a gradual higher CIP dosing up to 100 μg/L inhibited the TN removal efficiency, while the abundance of ARGs was still increased. Moreover, both the TN removal efficiency and the abundant ARGs were dwindled at 470 μg/L of CIP. As the CIP dose increased from 0 to 100 μg/L, the abundance of high molecular weight (MW) fractions (14,000 to 87,000 Da; 1000 to 14,000 Da) and humic/fulvic acid-like components in the soluble extracellular polymeric substances (HSS) decreased, with more increases of low MW (84-1000 Da; less than 84 Da) fractions and soluble microbial by-products in soluble extracellular polymeric substances (SMPS). Continuously increasing the CIP dose till 470 μg/L, an inverse trend of the changes of these organic components was noted, along with clear reductions of the microbial diversity and richness, and the abundance of key functional genes responsible for nitrogen removal. The predominance of functional gene amoA (related with ammonia oxidizing bacteria) was more significantly with more distribution of SMPS with relatively low MW and less distribution of HSS with relatively high MW, as well as polymer decomposing microorganisms such as Bryobacteraceae and the unclassified Saprospirales.
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Affiliation(s)
- Keke Xiao
- Engler-Bunte-Institut, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9, 76131, Karlsruhe, Germany; Environmental Science and Engineering Program, Guangdong Technion-Israel Institute of Technology, 241 Daxue Road, 515063, Shantou, Guangdong, China.
| | - Gudrun Abbt-Braun
- Engler-Bunte-Institut, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9, 76131, Karlsruhe, Germany
| | - Robert Pleitner
- Engler-Bunte-Institut, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9, 76131, Karlsruhe, Germany
| | - Harald Horn
- Engler-Bunte-Institut, Water Chemistry and Water Technology, Karlsruhe Institute of Technology, Engler-Bunte-Ring 9, 76131, Karlsruhe, Germany; DVGW Research Laboratories, Water Chemistry and Water Technology, Engler-Bunte-Ring 9, 76131, Karlsruhe, Germany
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Li J, Luo J, Li M, Wang C, Hu S, Lu K, Wang G. Splendidivirga corallicola gen. nov., sp. nov. and Agaribacillus aureus gen. nov., sp. nov., two bacteria isolated from coral Porites lutea, and proposal of Splendidivirgaceae fam. nov. Int J Syst Evol Microbiol 2024; 74. [PMID: 38739684 DOI: 10.1099/ijsem.0.006376] [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: 05/16/2024] Open
Abstract
The Bacteroidota is one of the dominant bacterial phyla in corals. However, the exact taxa of those coral bacteria under the Bacteroidota are still unclear. Two aerobic, Gram-stain-negative, non-motile rods, designated strains BMA10T and BMA12T, were isolated from stony coral Porites lutea collected from Weizhou Island, PR China. Global alignment of 16S rRNA gene sequences indicated that both strains are closest to species of Fulvivirga with the highest identities being lower than 93 %, and the similarity value between these two strains was 92.3 %. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that these two strains form an monophylogenetic lineage alongside the families Fulvivirgaceae, Reichenbachiellaceae, Roseivirgaceae, Marivirgaceae, Cyclobacteriaceae, and Cesiribacteraceae in the order Cytophagales, phylum Bacteroidota. The genomic DNA G+C contents of BMA10T and BMA12T were 38.4 and 41.9 mol%, respectively. The major polar lipids of BMA10T were phosphatidylethanolamine, unidentified aminophospholipid, four unidentified aminolipids, and five unidentified lipids. While those of BMA12T were phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids. The major cellular fatty acids detected in both isolates were iso-C15 : 0 and C16 : 1 ω5c. Carbohydrate-active enzyme analysis indicated these two strains may utilize coral mucus or chitin. Based on above characteristics, these two strains are suggested to represent two new species in two new genera of a new family in the order Cytophagales, for which the name Splendidivirga corallicola gen. nov., sp. nov., Agaribacillus aureus gen. nov., sp. nov. and Splendidivirgaceae fam. nov. are proposed. The type strain of S. corallicola is BMA10T (=MCCC 1K08300T=KCTC 102045T), and that for A. aureus is BMA12T (=MCCC 1K08309T=KCTC 102046T).
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Affiliation(s)
- Jin Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Jixin Luo
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Mi Li
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Chenyan Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Siyu Hu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Kun Lu
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
| | - Guanghua Wang
- Guangxi Key Laboratory on the Study of Coral Reefs in the South China Sea, Nanning 530004, PR China
- School of Marine Sciences, Guangxi University, Nanning 530004, PR China
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Lu H, Chen L, Huang L. Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae. Int J Syst Evol Microbiol 2024; 74. [PMID: 38629951 DOI: 10.1099/ijsem.0.006345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024] Open
Abstract
Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (DC2WT, DC25WT, and LKC2W) were isolated from streams in China. Comparisons based on the 16S rRNA gene sequences showed that these three strains share 16S rRNA gene sequence similarity values over 97.0 % with the species of genus Arcicella. There was confusion due to the fact that all species of genera Flectobacillus, Aquirufa, and Sandaracinomonas show 16S rRNA gene sequence similarity of over 90.0 % to the above three strains, but the genus Flectobacillus belongs to the family Spirosomataceae and the genera Aquirufa and Sandaracinomonas belong to the family Cytophagaceae. Observing the phylogenetic trees, strains DC2WT, DC25WT, and LKC2W cluster closely with the species of genus Arcicella, but some species within the families Spirosomataceae and Cytophagaceae are not monophyletic. The phylogenomic tree also showed a confused phylogenetic relationships among these non-monophyletic species. Combining the phylogenetic relationships and average nucleotide identity values, the current taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae were re-examined. The genera 'Chryseosolibacter', 'Dawidia', and Chryseotalea should belong to the new family Chryseotaleaceae fam. nov., the genera Arcicella, Flectobacillus, Pseudarcicella, Aquirufa, and Sandaracinomonas should belong to the new family Flectobacillaceae fam. nov., the genera Fluviimonas, Taeseokella, Arcticibacterium, Emticicia, Jiulongibacter, Marinilongibacter, Lacihabitans, and Leadbetterella should belong to the new family Leadbetterellaceae fam. nov., the genus Litoribacter should be reassigned to the family Cyclobacteriaceae, and the genera Arundinibacter and Tellurirhabdus should be reassigned to the family Spirosomataceae. Strains DC2WT and DC25WT are reported to represent two novel species of the genus Arcicella, for which the names Arcicella gelida sp. nov. (type strain DC2WT=GDMCC 1.3209T=KCTC 92559T) and Arcicella lustrica sp. nov. (type strain DC25WT=GDMCC 1.3210T=KCTC 92557T) are proposed.
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Affiliation(s)
- Huibin Lu
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Li Chen
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Linpei Huang
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
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Novoa EAM, Deshmukh UB, Oren A. Reclassification of Allomuricauda and Muricauda species as members of the genus Flagellimonas Bae et al. 2007 and emended description of the genus Flagellimonas. Int J Syst Evol Microbiol 2024; 74. [PMID: 38421264 DOI: 10.1099/ijsem.0.006286] [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: 03/02/2024] Open
Abstract
The recently proposed genus Allomuricauda Deshmukh and Oren 2023 is illegitimate because it includes the type species of the genera Flagellimonas Bae et al. 2007 and Spongiibacterium Yoon and Oh 2012, contravening Rule 51b(1) of the International Code of Nomenclature of Prokaryotes. As Flagellimonas Bae et al. 2007 is the earlier described genus, we here reclassify 36 species earlier described as belonging to the illegitimate genus Muricauda as species of Flagellimonas. We also present an emended description of the genus Flagellimonas.
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Affiliation(s)
- Eduardo A Molinari Novoa
- Chess Consulting & Project, Lima 15039, and 'La Molina' National Agrarian University, Lima 15024, Peru
| | - Umakant Bhoopati Deshmukh
- Institution of Higher Learning, Research and Specialized Studies Centre, Department of Botany, Janata Mahavidyalaya, Chandrapur 442 401, Maharashtra, India
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190401, Israel
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Arahal DR, Bull CT, Christensen H, Chuvochina M, Dedysh SN, Fournier PE, Konstantinidis KT, Parker CT, Ventosa A, Young P, Göker M. Judicial Opinion 129. Int J Syst Evol Microbiol 2024; 74. [PMID: 38376502 DOI: 10.1099/ijsem.0.006064] [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: 02/21/2024] Open
Abstract
Opinion 129 addresses the status of Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980). The name has the category 'division' and was included in the Approved Lists of Bacterial Names, although that category had previously been removed from the International Code of Nomenclature of Bacteria (1975 revision onwards). When the category 'phylum' was introduced into the International Code of Nomenclature of Prokaryotes (ICNP) in 2021, equivalence between 'phylum' and 'division' was not stipulated. Since the definition of the taxonomic categories and their relative order is one of the principal tasks of every code of nomenclature, the inclusion of Firmicutes corrig. Gibbons and Murray 1978 in the Approved Lists was an error. The name is either not validly published or illegitimate because its category is not covered by the ICNP. If Firmicutes corrig. Gibbons and Murray 1978 (Approved Lists 1980) was a validly published phylum name, it would be illegitimate because it would contravene Rule 8, which does not permit any deviation from the requirement to derive a phylum name from the name of the type genus. Since Firmicutes corrig. Gibbons and Murray 1978 is also part of a 'misfitting megaclassification' recognized in Opinion 128, the name is rejected, without any pre-emption regarding a hypothetically validly published name Firmicutes at the rank of phylum. Gracilicutes Gibbons and Murray 1978 (Approved Lists 1980) and Anoxyphotobacteriae Gibbons and Murray 1978 (Approved Lists 1980) are also rejected. The validly published phylum names have a variety of advantages over their not validly published counterparts and cannot be replaced with ad hoc names suggested in the literature. To ease the transition, it is recommended to mention the not validly published phylum names which strongly deviate in spelling from their validly published counterparts along with the latter in publications during the next years.
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Affiliation(s)
- David R Arahal
- Departamento de Microbiología y Ecología, Universitat de València, Valencia, Spain
| | - Carolee T Bull
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, 211 Buckhout Lab, University Park, PA 16802, USA
| | - Henrik Christensen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870 Frederiksberg C, Denmark
| | - Maria Chuvochina
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, QLD 4072, Australia
| | - Svetlana N Dedysh
- Research Center of Biotechnology RAS, Winogradsky Institute of Microbiology, Prospect 60-letya Octyabrya 7/2, Moscow 117312, Russia
| | | | - Konstantinos T Konstantinidis
- School of Civil & Environmental Engineering and School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Charles T Parker
- Department of Energy, Joint Genome Institute, Berkeley, CA 94720, USA
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, C/. Prof. Garcia Gonzalez 2, ES-41012 Sevilla, Spain
| | - Peter Young
- Department of Biology, University of York, York YO10 5DD, UK
| | - Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
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Shin JH, Tillotson G, MacKenzie TN, Warren CA, Wexler HM, Goldstein EJC. Bacteroides and related species: The keystone taxa of the human gut microbiota. Anaerobe 2024; 85:102819. [PMID: 38215933 DOI: 10.1016/j.anaerobe.2024.102819] [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] [Received: 09/06/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Microbial communities play a significant role in maintaining ecosystems in a healthy homeostasis. Presently, in the human gastrointestinal tract, there are certain taxonomic groups of importance, though there is no single species that plays a keystone role. Bacteroides spp. are known to be major players in the maintenance of eubiosis in the human gastrointestinal tract. Here we review the critical role that Bacteroides play in the human gut, their potential pathogenic role outside of the gut, and their various methods of adapting to the environment, with a focus on data for B. fragilis and B. thetaiotaomicron. Bacteroides are anaerobic non-sporing Gram negative organisms that are also resistant to bile acids, generally thriving in the gut and having a beneficial relationship with the host. While they are generally commensal organisms, some Bacteroides spp. can be opportunistic pathogens in scenarios of GI disease, trauma, cancer, or GI surgery, and cause infection, most commonly intra-abdominal infection. B. fragilis can develop antimicrobial resistance through multiple mechanisms in large part due to its plasticity and fluid genome. Bacteroidota (formerly, Bacteroidetes) have a very broad metabolic potential in the GI microbiota and can rapidly adapt their carbohydrate metabolism to the available nutrients. Gastrointestinal Bacteroidota species produce short-chain fatty acids such as succinate, acetate, butyrate, and occasionally propionate, as the major end-products, which have wide-ranging and many beneficial influences on the host. Bacteroidota, via bile acid metabolism, also play a role in in colonization-resistance of other organisms, including Clostridioides difficile, and maintenance of gut integrity.
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Affiliation(s)
- Jae Hyun Shin
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | | | | | - Cirle A Warren
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
| | - Hannah M Wexler
- GLAVAHCS, Los Angeles, CA, USA; David Geffen School of Medicine, University of California, Los Angeles, CA, USA.
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Wang J, Zhang Y, Ding Y, Zhang Y, Xu W, Zhang X, Wang Y, Li D. Adaptive characteristics of indigenous microflora in an organically contaminated high salinity groundwater. CHEMOSPHERE 2024; 349:140951. [PMID: 38101485 DOI: 10.1016/j.chemosphere.2023.140951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
Salinity, a critical factor, could directly or indirectly affect the microbial community structure and diversity. Changes in salinity levels act as environmental filters that influence the transformation of key microbial species. This study investigates the adaptive characteristics of indigenous microflora in groundwater in relation to external organic pollutants under high salinity stress. A highly mineralized shallow groundwater in Northwest China was conducted as the study area, and six representative sampling points were chosen to explore the response of groundwater hydrochemical parameters and microflora, as well as to identify the tolerance mechanisms of indigenous microflora to combined pollution. The results revealed that the dominant genera found in high salinity groundwater contaminated with organic pollutants possess the remarkable ability to degrade such pollutants even under challenging high salinity conditions, including Halomonas, Pseudomonas, Halothiobacillus, Sphingomonas, Lutibacter, Aquabacterium, Thiomicrospira, Aequorivita, etc. The hydrochemical factors, including total dissolved solids (TDS), sulfide, nitrite, nitrate, oxidation reduction potential (ORP), NH3-N, Na, Fe, benzene series, phenols, and halogenated hydrocarbons, demonstrated a significant influence on microflora. High levels of sulphate and sulfide in groundwater can exhibit dual effects on microflora. On one hand, these compounds can inhibit the growth and metabolism of microorganisms. On the other hand, they can also serve as effective electron donors/receptors during the microbial degradation of organic pollutants. Microorganisms exhibit resilience to the inhibitory effects of high salinity and organic pollutants via a series of tolerance mechanisms, such as strengthening the extracellular membrane barrier, enhancing the synthesis of relevant enzymes, initiating novel biochemical reactions, improving cellular self-healing capabilities, responding to unfavorable environmental conditions by migration, and enhancing the S cycle for the microbial metabolism of organic pollutants.
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Affiliation(s)
- Jili Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yuling Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China.
| | - Yang Ding
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yi Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Weiqing Xu
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Xinying Zhang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Yiliang Wang
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
| | - Dong Li
- Key Lab of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China; College of New Energy and Environment, Jilin University, Changchun, 130021, China; Institute of Water Resources and Environment, Jilin University, Changchun, 130021, China
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Pitt A, Lienbacher S, Schmidt J, Neumann-Schaal M, Wolf J, Hahn MW. Description of a new freshwater bacterium Aquirufa regiilacus sp. nov., classification of the genera Aquirufa, Arundinibacter, Sandaracinomonas, and Tellurirhabdus to the family Spirosomataceae, classification of the genus Chryseotalea to the family Fulvivirgaceae and Litoribacter to the family Cyclobacteriaceae, as well as classification of Litoribacter alkaliphilus as a later heterotypic synonym of Litoribacter ruber. Arch Microbiol 2024; 206:79. [PMID: 38280955 PMCID: PMC10821818 DOI: 10.1007/s00203-023-03801-8] [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: 11/01/2023] [Revised: 12/05/2023] [Accepted: 12/16/2023] [Indexed: 01/29/2024]
Abstract
Strains LEOWEIH-7CT and LEPPI-3A were isolated from the Leopoldskroner Weiher, a lake located in the city of Salzburg, Austria. 16S rRNA gene similarities and phylogenetic reconstructions with 16S rRNA gene sequences as well as based on genome sequences revealed that the new strains belong to the A. antheringensis branch of the genus Aquirufa. Calculated whole-genome average nucleotide identity (gANI) and digital DNA-DNA hybridization (dDDH) values with the closely related type strains showed that the two strains represent a single new species. The strains grew aerobically and chemoorganotrophically, and the cells were rod shaped, on average 0.8 µm long and 0.3 µm wide, red pigmented and motile by gliding. The genome size of both strains was 2.6 Mbp and the G+C value was 41.9%. The genomes comprised genes predicted for the complete light-harvesting rhodopsin system and various carotenoids. We proposed to establish the name Aquirufa regiilacus sp. nov. for strain LEOWEIH-7CT (=DSM 116390T = JCM 36347T) as the type strain. Strain LEPPI-3A (=DSM 116391 = JCM 36348) also belongs to this new species. The calculated genome-based phylogenetic tree revealed that Aquirufa and some other genera currently allocated in the family Cytophagaceae need a reclassification. Aquirufa, Arundinibacter, Sandaracinomonas, and Tellurirhabdus should be designated to the family Spirosomataceae, the genus Chryseotalea to the family Fulvivirgaceae, and the genus Litoribacter to the family Cyclobacteriaceae. Furthermore, based on calculated gANI and dDDH values, Litoribacter alkaliphilus should be reclassified as a later heterotypic synonym of Litoribacter ruber.
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Affiliation(s)
- Alexandra Pitt
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria.
| | - Stefan Lienbacher
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria
| | - Johanna Schmidt
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria
| | - Meina Neumann-Schaal
- Chemical Analytics and Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Jacqueline Wolf
- Chemical Analytics and Metabolomics, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Martin W Hahn
- Research Department for Limnology, Universität Innsbruck, Mondseestrasse 9, 5310, Mondsee, Austria
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Shaikh SS, Jhala D, Patel A, Chettiar SS, Ghelani A, Malik A, Sengupta P. In-silico analysis of probiotic attributes and safety assessment of probiotic strain Bacillus coagulans BCP92 for human application. Lett Appl Microbiol 2024; 77:ovad145. [PMID: 38148133 DOI: 10.1093/lambio/ovad145] [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] [Received: 11/09/2023] [Revised: 12/16/2023] [Accepted: 12/25/2023] [Indexed: 12/28/2023]
Abstract
The whole genome sequence (WGS) of Bacillus coagulans BCP92 is reported along with its genomic analysis of probiotics and safety features. The identification of bacterial strain was carried out using the 16S rDNA sequencing method. Furthermore, gene-related probiotic features, safety assessment (by in vitro and in silico), and genome stability were also studied using the WGS analysis for the possible use of the bacterial strain as a probiotic. From the BLAST analysis, bacterial strain was identified as Bacillus (Heyndrickxia) coagulans. WGS analysis indicated that the genome consists of a 3 475 658 bp and a GC-content of 46.35%. Genome mining of BCP92 revealed that the strain is consist of coding sequences for d-lactate dehydrogenase and l-lactate dehydrogenases, 36 genes involved in fermentation activities, 29 stress-responsive as well as many adhesions related genes. The genome, also possessing genes, is encoded for the synthesis of novel circular bacteriocin. Using an in-silico approach for the bacterial genome study, it was possible to determine that the Bacillus (Heyndrickxia) coagulans strain BCP92 contains genes that are encoded for the probiotic abilities and did not harbour genes that are risk associated, thus confirming the strain's safety and suitability as a probiotic to be used for human application.
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Affiliation(s)
- Sohel S Shaikh
- Pellucid Lifesciences Pvt Ltd, Plot No.:3538, Phase-4, GIDC Industrial Estate, Chhatral, Gandhinagar 382729, India
| | - Devendrasinh Jhala
- Zoology Department, School of Sciences, Gujarat University, Ahmedabad 380009, India
| | - Alpesh Patel
- Genexplore Diagnostics & Research Centre Pvt Ltd, 1201 to 1210, Iconic Shyamal, Shyamal, Ahmedabad 380015, India
| | - Shiva Shankaran Chettiar
- Genexplore Diagnostics & Research Centre Pvt Ltd, 1201 to 1210, Iconic Shyamal, Shyamal, Ahmedabad 380015, India
| | - Anjana Ghelani
- Shree Ramkrishna Institute of Computer Education and Applied Sciences, M.T.B. College Campus, B/h P.T. Science College, Opp. Chowpati, Athwalines, Surat 395001, India
| | - Anis Malik
- Pellucid Lifesciences Pvt Ltd, Plot No.:3538, Phase-4, GIDC Industrial Estate, Chhatral, Gandhinagar 382729, India
| | - Priyajit Sengupta
- Pellucid Lifesciences Pvt Ltd, Plot No.:3538, Phase-4, GIDC Industrial Estate, Chhatral, Gandhinagar 382729, India
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Sababadichetty L, Miltgen G, Vincent B, Guilhaumon F, Lenoble V, Thibault M, Bureau S, Tortosa P, Bouvier T, Jourand P. Microplastics in the insular marine environment of the Southwest Indian Ocean carry a microbiome including antimicrobial resistant (AMR) bacteria: A case study from Reunion Island. MARINE POLLUTION BULLETIN 2024; 198:115911. [PMID: 38103498 DOI: 10.1016/j.marpolbul.2023.115911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/13/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
The increasing threats to ecosystems and humans from marine plastic pollution require a comprehensive assessment. We present a plastisphere case study from Reunion Island, a remote oceanic island located in the Southwest Indian Ocean, polluted by plastics. We characterized the plastic pollution on the island's coastal waters, described the associated microbiome, explored viable bacterial flora and the presence of antimicrobial resistant (AMR) bacteria. Reunion Island faces plastic pollution with up to 10,000 items/km2 in coastal water. These plastics host microbiomes dominated by Proteobacteria (80 %), including dominant genera such as Psychrobacter, Photobacterium, Pseudoalteromonas and Vibrio. Culturable microbiomes reach 107 CFU/g of microplastics, with dominance of Exiguobacterium and Pseudomonas. Plastics also carry AMR bacteria including β-lactam resistance. Thus, Southwest Indian Ocean islands are facing serious plastic pollution. This pollution requires vigilant monitoring as it harbors a plastisphere including AMR, that threatens pristine ecosystems and potentially human health through the marine food chain.
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Affiliation(s)
- Loik Sababadichetty
- Université de La Réunion, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France; CHU, Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400 Saint-Denis, La Réunion, France
| | - Guillaume Miltgen
- CHU, Laboratoire de Bactériologie, CHU Félix Guyon, Allée des Topazes, 97400 Saint-Denis, La Réunion, France; Université de La Réunion, UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, 97490 Ste Clotilde, La Réunion, France
| | - Bryan Vincent
- CIRAD, UMR040 LSTM, Campus Agro Environnemental Caraïbe, BP 214-97285, Cedex 2 le Lamentin, Martinique, Antilles Françaises, France
| | - François Guilhaumon
- IRD, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France
| | - Veronique Lenoble
- Université de Toulon, Aix Marseille Université, CNRS, IRD, UMR MIO, 83 Toulon, France
| | - Margot Thibault
- Université de La Réunion, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France; The Ocean Cleanup, Rotterdam, the Netherlands; CNRS, Université Toulouse III, Laboratoire des Interactions Moléculaires et Réactivité Chimique et Photochimique (IMRCP), UMR 5623, Toulouse, France
| | - Sophie Bureau
- Université de La Réunion, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France
| | - Pablo Tortosa
- Université de La Réunion, UMR PIMIT Processus Infectieux en Milieu Insulaire Tropical, CNRS 9192, INSERM 1187, IRD 249, Plateforme de recherche CYROI, 2 rue Maxime Rivière, 97490 Ste Clotilde, La Réunion, France
| | - Thierry Bouvier
- UMR MARBEC, Université Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Philippe Jourand
- IRD, UMR ENTROPIE, 15 Avenue René Cassin, CS 92003, 97744 Saint Denis Cedex 9, La Réunion, France.
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Liu W, Cong B, Lin J, Liu S, Deng A, Zhao L. Taxonomic identification and temperature stress tolerance mechanisms of Aequorivita marisscotiae sp. nov. Commun Biol 2023; 6:1186. [PMID: 37990058 PMCID: PMC10663628 DOI: 10.1038/s42003-023-05559-7] [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: 07/04/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
The deep sea harbours microorganisms with unique life characteristics and activities due to adaptation to particular environmental conditions, but the limited sample collection and pure culture techniques available constrain the study of deep-sea microorganisms. In this study, strain Ant34-E75 was isolated from Antarctic deep-sea sediment samples and showed the highest 16 S rRNA gene sequence similarity (97.18%) with the strain Aequorivita viscosa 8-1bT. Strain Ant34-E75 is psychrotrophic and can effectively increase the cold tolerance of Chlamydomonas reinhardtii (a model organism). Subsequent transcriptome analysis revealed multiple mechanisms involved in the Ant34-E75 response to temperature stress, and weighted gene co-expression network analysis (WGCNA) showed that the peptidoglycan synthesis pathway was the key component. Overall, this study provides insights into the characteristics of a deep-sea microorganism and elucidates mechanisms of temperature adaptation at the molecular level.
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Affiliation(s)
- Wenqi Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Bailin Cong
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China.
| | - Jing Lin
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Shenghao Liu
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Aifang Deng
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, China
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12
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Wang M, Zheng N, Li X, Zhao K, Xie BB. Enrichment Pretreatment Expands the Microbial Diversity Cultivated from Marine Sediments. Microorganisms 2023; 11:2771. [PMID: 38004782 PMCID: PMC10673404 DOI: 10.3390/microorganisms11112771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
The majority of the microbial diversity in nature has not been recovered through cultivation. Enrichment is a classical technique widely used in the selective cultivation of specific taxa. Whether enrichment is suitable for cultivation studies that aim to recover large numbers of species remains little explored. To address this issue, we evaluated the potential of enrichment pretreatment in the cultivation of bacteria from marine sediments. Upon obtaining and classifying a total of 943 pure cultures from chitin and cellulose enrichment pretreatment systems and a control system, our results showed that species obtained using enrichment pretreatment differed greatly from those without enrichment. Multiple enrichment media and different enrichment times increased the number of cultivated species in a sample. Amplicon sequencing showed that the increased relative abundance during pretreatment contributed greatly to bacterial cultivation. The testing of degradation abilities against chitin and cellulose and the whole-genome sequencing of representative strains suggested that microorganism-microorganism interactions play roles in the expanded diversity of cultivated bacteria. This study provides new insights into the abilities of enrichment in exploring cultivable diversity and mining microbial resources.
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Affiliation(s)
| | | | | | | | - Bin-Bin Xie
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, China; (M.W.); (N.Z.); (X.L.); (K.Z.)
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13
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English J, Newberry F, Hoyles L, Patrick S, Stewart L. Genomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species. J Med Microbiol 2023; 72. [PMID: 37910167 DOI: 10.1099/jmm.0.001768] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B. fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.
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Affiliation(s)
- Jamie English
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
| | - Fiona Newberry
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Sheila Patrick
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
| | - Linda Stewart
- Institute for Global Food Security, School of Biological Sciences, Queen's University, Belfast, UK
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Lu H, Li P, Chen L, Chen G. Flectobacillus longus sp. nov. and Flectobacillus rivi sp. nov., isolated from streams in China and reclassification of Flectobacillus rhizosphaerae as a synonym of Flectobacillus roseus. Int J Syst Evol Microbiol 2023; 73. [PMID: 37917534 DOI: 10.1099/ijsem.0.006148] [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: 11/04/2023] Open
Abstract
Three Gram-stain-negative, aerobic, rod-shaped, non-motile strains (LYT7WT, DC10W and LFS242WT) were isolated from streams in PR China. Comparisons based on the 16S rRNA gene sequences showed that these three strains showed high 16S rRNA gene sequence similarity to Flectobacillus roseus GFA-11T (99.2, 98.8 and 99.8 %, respectively) and Flectobacillus rhizosphaerae JC289T (98.8, 98.6 and 99.4 %, respectively), and less than 96.6 % to other species of the genus Flectobacillus. The phylogenetic tree reconstructed based on the 16S rRNA gene sequences showed that strains LYT7WT, DC10W, LFS242WT, F. roseus GFA-11T and F. rhizosphaerae JC289T formed a tight cluster. The phylogenomic tree also supported the above robust phylogenetic relationships. The calculated OrthoANIu and digital DNA-DNA hybridization values between strains LYT7WT and DC10W were 95.2 % and 61.9 %, respectively. Although these values are located in the transition region for species demarcation, the similar physiological and genotypic characteristics supported that strains LYT7WT and DC10W should belong to the same species. The pairwise OrthoANIu and digital DNA-DNA hybridization values between strain LFS242WT and its related strains were less than 91.8 and 45.3 %, respectively, indicating that strain LFS242WT should represent an independent novel species of the genus Flectobacillus. It should be noticed that the pairwise OrthoANIu and digital DNA-DNA hybridization values between strains F. roseus LMG 24501T and F. rhizosphaerae KCTC 42575T were 96.9 and 73.1 %, respectively. The similar physiological and genotypic characteristics also supported that F. rhizosphaerae Ramaprasad et al. 2015 should be a synonym of F. roseus Sheu et al. 2009. Combining the above descriptions, strains LYT7WT, DC10W and LFS242WT should represent two novel species of the genus Flectobacillus, for which the names Flectobacillus longus sp. nov. (type strain LYT7WT=GDMCC 1.3222T=KCTC 92561T) and Flectobacillus rivi sp. nov. (type strain LFS242WT=GDMCC 1.3223T=KCTC 92562T) are proposed.
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Affiliation(s)
- Huibin Lu
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Ping Li
- College of Environment and Resource, Xichang University, Xichang 615000, PR China
| | - Li Chen
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
| | - Guangjie Chen
- Yunnan Key Laboratory of Plateau Geographical Process and Environmental Changes, Faculty of Geography, Yunnan Normal University, Kunming 650500, PR China
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Liu B, Wan Y, Liu L, Lv Y, Zhang Q, Cheng D, He J, Shen Q. Shiella aurantiaca gen. nov., sp. nov., a novel bacterium isolated from activated sludge, and proposal of Shiellaceae fam. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37991220 DOI: 10.1099/ijsem.0.006175] [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: 11/23/2023] Open
Abstract
A novel Gram-stain-negative, long rod-shaped, aerobic, non-motile, non-spore-forming and orange-pigmented bacterium, designated LB-30T, was isolated from activated sludge. Growth was observed at 15-40 °C (optimum 30 °C), pH 6.0-9.0 (optimum 7.0) and salinities of 0-3.0 % (w/v; optimum 2.0 %). LB-30T showed less than 89.9 % sequence similarities to the recognized taxa of the order Cytophagales. The results of phylogenetic analysis based on 16S rRNA gene sequences and phylogenomic tree indicated that LB-30T formed a distinct lineage within the order Cytophagales. The average amino acid identity (AAI) values between LB-30T and members of the related families Cyclobacteriaceae, Fulvivirgaceae, Roseivirgaceae, Reichenbachiellaceae, Cesiribacteraceae, Cytophagaceae and Hymenobacteraceae in the order Cytophagales were 50.5-54.6 %. The sole respiratory quinone of LB-31T was menaquinone 7 (MK-7). The major polar lipids were phosphatidylethanolamine, aminolipid and four unidentified lipids. The major fatty acids were iso-C15 : 0, iso-C15 : 1G and iso-C17 : 0 3-OH. The DNA G+C content was 43.8 mol%, calculated from the genome sequence. On the basis of differences in the phenotypic, physiological and biochemical characteristics, and distinct phylogenetic relationships, strain LB-30T is proposed to represent a novel species in a novel genus for which the name Shiella aurantiaca gen. nov., sp. nov is proposed, within a novel family Shiellaceae fam. nov. of the order Cytophagales. The type strain is LB-30T (=GDMCC 1.3629T= KCTC 92689T).
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Affiliation(s)
- Bin Liu
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi 330022, PR China
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yingying Wan
- College of Life Sciences, Jiangxi Normal University, Nanchang, Jiangxi 330022, PR China
| | - Le Liu
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Yu Lv
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Qi Zhang
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Dan Cheng
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Jian He
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
| | - Qirong Shen
- Agricultural Microbial Resources Protection and Germplasm Innovation and Utilization Center of Jiangsu Province, Nanjing, Jiangsu 210095, PR China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
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16
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Wang Y, Zhang X, Tang G, Deng P, Qin Y, Han J, Wang S, Sun X, Li D, Chen Z. The causal relationship between gut microbiota and bone mineral density: a Mendelian randomization study. Front Microbiol 2023; 14:1268935. [PMID: 37937216 PMCID: PMC10625988 DOI: 10.3389/fmicb.2023.1268935] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
Background The gut microbiota has emerged as an intriguing and potentially influential factor in regulating bone health. However, the causal effect of the gut microbiota on bone mineral density (BMD) appears to differ throughout various life stages. Methods We conducted a Mendelian randomization (MR) analysis to investigate the potential causal relationship between gut microbiota and BMD in five distinct age groups: 0-15, 15-30, 30-45, 45-60, and 60 years and older. The analysis employed three different methods, namely MR-Egger, weighted median, and Inverse-variance weighting, to ensure the robustness of our findings, a series of sensitivity analyses were also conducted, such as horizontal pleiotropy tests, heterogeneity tests, and leave-one-out sensitivity tests. Results In the age group of 0-15 years, Eubacterium_fissicatena_group and Eubacterium_hallii_group were identified as risk factors for BMD. During the 15-30 age group, Phascolarctobacterium, Roseburia, and Ruminococcaceae_UCG_003 were found to be protective factors for BMD. In the 30-45 age group, Lachnospira genus demonstrated a protective effect on BMD, while Barnesiella and Lactococcus were identified as risk factors for BMD. Moving on to the 45-60 age group, Eubacterium_ventriosum_group, Lachnospiraceae_UCG_004, and Subdoligranulum were observed to be protective factors for BMD, while Eubacterium_coprostanoligenes_group, Fusicatenibacter, and Lactococcus were associated with an increased risk of BMD. In individuals aged 60 years and older, Fusicatenibacter and Ruminococcaceae_UCG_002 were also noted as risk factors for BMD. Conversely, Eubacterium_ruminantium_group, Ruminococcus_gauvreauii_group, Alistipes, and Coprococcus_3 were found to be protective factors for BMD, whereas Barnesiella and Sellimonas were identified as risk factors for BMD. Conclusion A robust causal relationship between gut microbiota and bone mineral density (BMD) exists throughout all stages of life, with Firmicutes phylum being the primary group associated with BMD across age groups. Gut microbiota linked with BMD primarily belong to the Firmicutes phylum across age groups. The diversity of gut microbiota phyla associated with BMD depicts relatively stable patterns during the ages of 0-45 years. However, for individuals aged 45 years and above, there is an observed increase in the number of gut microbiota species linked with BMD, and by the age of 60 years, a trend toward an increase in the Bacteroidetes phylum categories is proposed.
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Affiliation(s)
- Ying Wang
- Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Xuejian Zhang
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Guangjun Tang
- Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Pin Deng
- Institute of Basic Theory of Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yuyan Qin
- Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Jinglu Han
- Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Shulong Wang
- Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Xiaojie Sun
- Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Dongxiao Li
- Beijing University of Chinese Medicine, Beijing, China
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
| | - Zhaojun Chen
- Beijing University of Chinese Medicine Third Affiliated Hospital, Beijing, China
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Liu JC, Ye YQ, Tan XY, Du ZJ, Ye MQ. Description of Aequorivita aurantiaca sp. nov. Isolated from Coastal Sediment, and Comparative Genomic Analysis and Biogeographic Distribution of the Genus Aequorivita. Microorganisms 2023; 11:2518. [PMID: 37894175 PMCID: PMC10608841 DOI: 10.3390/microorganisms11102518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/19/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
A novel Gram-stain-negative, facultatively anaerobic, and non-motile bacterial strain, designated SDUM287046T, was isolated from the coastal sediments of Jingzi Port of Weihai, China. Cells of strain SDUM287046T were rod-shaped with widths of 0.4-0.5 μm and lengths of 0.7-1.4 μm and could produce flexirubin-type pigments. Optimum growth of strain SDUM287046T occurred at 33-35 °C, pH 7.0, and with 2% (w/v) NaCl. Oxidase activity was negative, but catalase activity was positive. Phylogenetic analysis based on 16S rRNA gene sequence revealed that strain SDUM287046T was most closely related to Aequorivita aquimaris D-24T (98.3%). The main cellular fatty acids were iso-C15:0, anteiso-C15:0, iso-C17:0 3-OH, and summed feature 9 (comprised of iso-C17:1 ω9c and/or C16:0 10-methyl). The sole respiratory quinone was MK-6. The polar lipids consisted of phosphatidylethanolamine (PE), one aminolipid (AL), three unidentified glycolipids (GL), and three unidentified lipids (L). The DNA G + C content was 39.3 mol%. According to the integrated results of phylogenetic, physiological, biochemical, and chemotaxonomic characteristics, we propose that strain SDUM287046T represents a novel species of the genus Aequorivita, for which the name Aequorivita aurantiaca sp. nov. is proposed. The type strain is SDUM287046T (=KCTC 92754T = MCCC 1H01418T). Comparative genomic analysis showed that the 16 Aequorivita species shared 1453 core genes and differed mainly in amino acid metabolism, cofactor metabolism, and vitamin metabolism. Biogeographic distribution analysis indicated that the marine environments were the primary habitat of Aequorivita bacteria.
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Affiliation(s)
- Jun-Cheng Liu
- SDU-ANU Joint Science College, Shandong University, Weihai 264209, China;
| | - Yu-Qi Ye
- Marine College, Shandong University, Weihai 264209, China; (Y.-Q.Y.); (X.-Y.T.); (Z.-J.D.)
| | - Xin-Yun Tan
- Marine College, Shandong University, Weihai 264209, China; (Y.-Q.Y.); (X.-Y.T.); (Z.-J.D.)
| | - Zong-Jun Du
- Marine College, Shandong University, Weihai 264209, China; (Y.-Q.Y.); (X.-Y.T.); (Z.-J.D.)
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai 264209, China
| | - Meng-Qi Ye
- Marine College, Shandong University, Weihai 264209, China; (Y.-Q.Y.); (X.-Y.T.); (Z.-J.D.)
- Weihai Research Institute of Industrial Technology, Shandong University, Weihai 264209, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518057, China
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18
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Moreno IJ, Brahamsha B, Donia MS, Palenik B. Diverse Microbial Hot Spring Mat Communities at Black Canyon of the Colorado River. MICROBIAL ECOLOGY 2023; 86:1534-1551. [PMID: 36757423 PMCID: PMC10497668 DOI: 10.1007/s00248-023-02186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The thermophilic microbial mat communities at hot springs in the Black Canyon of the Colorado River, thought to harbor the protistan human pathogen Naegleria fowleri, were surveyed using both culture-independent and -dependent methods to further understand the ecology of these hot spring microbiomes. Originating from Lake Mead source water, seven spring sites were sampled, varying in temperature from 25 to 55 °C. Amplicon-based high-throughput sequencing of twelve samples using 16S rRNA primers (hypervariable V4 region) revealed that most mats are dominated by cyanobacterial taxa, some but not all similar to those dominating the mats at other studied hot spring systems. 18S rRNA amplicon sequencing (V9 region) demonstrated a diverse community of protists and other eukaryotes including a highly abundant amoebal sequence related to Echinamoeba thermarum. Additional taxonomic and diversity metric analyses using near full-length 16S and 18S rRNA gene sequencing allowed a higher sequence-based resolution of the community. The mat sequence data suggest a major diversification of the cyanobacterial orders Leptolyngbyales, as well as microdiversity among several cyanobacterial taxa. Cyanobacterial isolates included some representatives of ecologically abundant taxa. A Spearman correlation analysis of short-read amplicon sequencing data supported the co-occurrences of populations of cyanobacteria, chloroflexi, and bacteroidetes providing evidence of common microbial co-occurrences across the Black Canyon hot springs.
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Affiliation(s)
- Ivan J Moreno
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Bianca Brahamsha
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Mohamed S Donia
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Brian Palenik
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
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Zhang X, Feng GD, Liu Y, Yang F, Li Y, Deng X, Zhu H, Yao Q. Description of Xanthocytophaga agilis sp. nov. and Xanthocytophaga flavus sp. nov. of the new genus Xanthocytophaga gen. nov and the proposal of Rhodocytophagaceae fam. nov. within the order Cytophagales. Arch Microbiol 2023; 205:345. [PMID: 37768397 DOI: 10.1007/s00203-023-03685-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
Four Gram-staining-negative, aerobic, yellow-pigmented and rod-shaped bacteria, named strains BD1B2-1T, NT2B1T, YF14B1 and DM2B3-1, were isolated from four rhizosphere soil samples of banana in China. Comparison of the 16S rRNA gene sequences showed that all these strains were most closely related to an invalidly published species, 'Rhodocytophaga rosea' 172606-1, with similarities ranging from 87.7 to 88.0%. According to the phylogenomic analysis, the four strains were clustered in an independent lineage and closely related to the genus Rhodocytophaga. The genomic sizes of these strains were approximately 9.49-9.77 Mbp with the DNA G + C contents of 38.8-39.0 mol%. They all contained C16:1 ω5c, iso-C15:0 and iso-C17:0 3-OH as the major fatty acids and menaquinone 7 as the only respiratory quinone. They all had phosphatidylethanolamine as the major polar lipids. Based on phenotypic and phylogenomic characteristics, the four strains should represent two novel species within a novel genus, for which the names Xanthocytophaga agilis gen. nov., sp. nov. (BD1B2-1T = GDMCC 1.2890T = JCM 35374T) and Xanthocytophaga flavus sp. nov. (NT2B1T = GDMCC 1.2889T = JCM 35375T) are proposed; the former is assigned as the type species of the novel genus Xanthocytophaga gen. nov. In addition, based on the phenotypic and phylogenomic data, we proposed to reclassify the existing genus Rhodocytophaga in the family Cytophagaceae into a novel family Rhodocytophagaceae fam. nov. The novel family consists of the type genus Rhodocytophaga and the novel genus Xanthocytophaga.
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Affiliation(s)
- Xianjiao Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Horticulture, South China Agricultural University, Guangzhou, 510642, People's Republic of China
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Guang-Da Feng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yang Liu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Fan Yang
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Yanxuan Li
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Xiaoqin Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
| | - Qing Yao
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, People's Republic of China.
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Deshmukh UB, Oren A. Proposal of Allomuricauda gen. nov. and Allofranklinella gen. nov. as replacement names for the illegitimate prokaryotic generic names Muricauda and Franklinella, respectively. Int J Syst Evol Microbiol 2023; 73. [PMID: 37747448 DOI: 10.1099/ijsem.0.006023] [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: 09/26/2023] Open
Abstract
The prokaryotic generic names Muricauda Bruns et al. 2001 and Franklinella Bernard et al. 2022 are illegitimate because they are later homonyms of the genus names Muricauda Small 1903 (synonym of Arisaema; Tracheophyta - Liliopsida - Araceae) and Franklinella Stewart and Hendrix 1945 (a Devonian ostracod genus) and Franklinella Lenz 1973 (a Devonian brachiopod genus), respectively (Principle 2 and Rule 51b(4) of the International Code of Nomenclature of Prokaryotes). We therefore propose the replacement generic names Allomuricauda and Allofranklinella, with type species Allomuricauda ruestringensis and Allofrankinella schreckenbergeri, respectively.
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Affiliation(s)
- Umakant Bhoopati Deshmukh
- Department of Botany, Institution of Higher Learning, Research and Specialized Studies Centre, Janata Mahavidyalaya, Chandrapur 442 401, Maharashtra, India
| | - Aharon Oren
- Department of Plant and Environmental Sciences, The Institute of Life Sciences, The Hebrew University of Jerusalem, Edmund J. Safra Campus, Jerusalem 9190401, Israel
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21
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Kong W, Qiu L, Ishii S, Jia X, Su F, Song Y, Hao M, Shao M, Wei X. Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems. ISME COMMUNICATIONS 2023; 3:81. [PMID: 37596350 PMCID: PMC10439144 DOI: 10.1038/s43705-023-00286-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/20/2023]
Abstract
Soil microbiomes play important roles in supporting agricultural ecosystems. However, it is still not well-known how soil microbiomes and their functionality respond to fertilization in various cropping systems. Here we examined the effects of 36 years of phosphorus, nitrogen, and manure application on soil bacterial communities, functionality and crop productivity in three contrasting cropping systems (i.e., continuous leguminous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation of winter wheat + millet - pea - winter wheat (GLR)) in a highland region of China's Loess Plateau. We showed that long-term fertilization significantly affected soil bacterial communities and that the effects varied with cropping system. Compared with the unfertilized control, fertilization increased soil bacterial richness and diversity in the leguminous AC system, whereas it decreased those in the GLR system. Fertilization, particularly manure application, enlarged the differences in soil bacterial communities among cropping systems. Soil bacterial communities were mostly affected by the soil organic carbon and nitrogen contents in the WC and GLR systems, but by the soil available phosphorous content in the AC system. Crop productivity was closely associated with the abundance of fertilization-responsive taxa in the three cropping systems. Our study highlights that legume and non-legume cropping systems should be disentangled when assessing the responses of soil microbial communities to long-term fertilizer application.
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Affiliation(s)
- Weibo Kong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Liping Qiu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, 55108, USA
| | - Xiaoxu Jia
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, 100101, Beijing, China
| | - Fuyuan Su
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Yu Song
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- College of Natural Resources and Environment, Northwest A&F University, Yangling, 712100, China
| | - Mingde Hao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
| | - Mingan Shao
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China
| | - Xiaorong Wei
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- Research Center of Soil and Water Conservation and Ecological Environment, Ministry of Education, Chinese Academy of Sciences, Yangling, 712100, China.
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, Shaanxi, China.
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22
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Romanenko L, Otstavnykh N, Kurilenko V, Velansky P, Eremeev V, Mikhailov V, Isaeva MP. Description and genome-wide analysis of Profundicola chukchiensis gen. nov., sp. nov., marine bacteria isolated from bottom sediments of the Chukchi Sea. PLoS One 2023; 18:e0287346. [PMID: 37494411 PMCID: PMC10370774 DOI: 10.1371/journal.pone.0287346] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 06/04/2023] [Indexed: 07/28/2023] Open
Abstract
Two Gram-negative, aerobic halophilic non-motile strains designated KMM 9713 and KMM 9724T were isolated from the bottom sediments sampled from the Chukchi Sea in the Arctic Ocean, Russia. The novel strains grew in 0.5-5% NaCl, at 7-42°C, and pH 5.5-10.5. Phylogenetic analyses based on 16S rRNA gene and whole genome sequences revealed that strains KMM 9713 and KMM 9724T were close to each other and shared the highest 16S rRNA gene sequence similarity of 91.28% with the type strain Ornithobacterium rhinotracheale DSM 15997T and 90.15-90.92% with the members of the genus Empedobacter in the family Weeksellaceae. Phylogenetic trees indicated that strains KMM 9713 and KMM 9724T formed a distinct line adjacent to their relative O. rhinotracheale DSM 15997T. The average nucleotide identity values between strain KMM 9724T and O. rhinotracheale DSM 15997T, Empedobacter brevis NBRC 14943T, and Moheibacter sediminis CGMCC 1.12708T were 76.73%, 75.78%, and 74.65%, respectively. The novel strains contained the predominant menaquinone MK-6 and the major fatty acids of iso-C17:0 3-OH, iso-C15:0 followed by iso-C17:1ω6. Polar lipids consisted of phosphatidylethanolamine, one an unidentified aminophospholipid, two unidentified aminolipids, and two or three unidentified lipids. The DNA G+C contents of 34.5% and 34.7% were calculated from genome sequence of the strains KMM 9713 and KMM 9724T, respectively. Based on the phylogenetic evidence and distinctive phenotypic characteristics, strains KMM 9713 and KMM 9724T are proposed to be classified as a novel genus and species Profundicola chukchiensis gen. nov., sp. nov. The type strain of Profundicola chukchiensis gen. nov., sp. nov. is strain KMM 9724T (= KACC 22806T).
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Affiliation(s)
- Lyudmila Romanenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Nadezhda Otstavnykh
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Valeriya Kurilenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Peter Velansky
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Viacheslav Eremeev
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Valery Mikhailov
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
| | - Marina P Isaeva
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch, Russian Academy of Sciences, Vladivostok, Russia
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Santos-Pereira C, Sousa J, Costa ÂMA, Santos AO, Rito T, Soares P, Franco-Duarte R, Silvério SC, Rodrigues LR. Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples. Appl Microbiol Biotechnol 2023:10.1007/s00253-023-12627-9. [PMID: 37417976 PMCID: PMC10390414 DOI: 10.1007/s00253-023-12627-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 07/08/2023]
Abstract
The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.
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Affiliation(s)
- Cátia Santos-Pereira
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Joana Sousa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Ângela M A Costa
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Andréia O Santos
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
| | - Teresa Rito
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Pedro Soares
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Ricardo Franco-Duarte
- CBMA-Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- IB-S-Institute of Science and Innovation for Bio-Sustainability, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara C Silvério
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal.
| | - Lígia R Rodrigues
- CEB-Centre of Biological Engineering, Universidade Do Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS-Associate Laboratory, Guimarães, Braga, Portugal
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24
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Mourgela RN, Kioukis A, Pourjam M, Lagkouvardos I. Large-Scale Integration of Amplicon Data Reveals Massive Diversity within Saprospirales, Mostly Originating from Saline Environments. Microorganisms 2023; 11:1767. [PMID: 37512939 PMCID: PMC10384058 DOI: 10.3390/microorganisms11071767] [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: 04/14/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
The order Saprospirales, a group of bacteria involved in complex degradation pathways, comprises three officially described families: Saprospiraceae, Lewinellaceae, and Haliscomenobacteraceae. These collectively contain 17 genera and 31 species. The current knowledge on Saprospirales diversity is the product of traditional isolation methods, with the inherited limitations of culture-based approaches. This study utilized the extensive information available in public sequence repositories combined with recent analytical tools to evaluate the global evidence-based diversity of the Saprospirales order. Our analysis resulted in 1183 novel molecular families, 15,033 novel molecular genera, and 188 K novel molecular species. Of those, 7 novel families, 464 novel genera, and 1565 species appeared in abundances at ≥0.1%. Saprospirales were detected in various environments, such as saline water, freshwater, soil, various hosts, wastewater treatment plants, and other bioreactors. Overall, saline water was the environment showing the highest prevalence of Saprospirales, with bioreactors and wastewater treatment plants being the environments where they occurred with the highest abundance. Lewinellaceae was the family containing the majority of the most prevalent species detected, while Saprospiraceae was the family with the majority of the most abundant species found. This analysis should prime researchers to further explore, in a more targeted way, the Saprospirales proportion of microbial dark matter.
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Affiliation(s)
- Rafaila Nikola Mourgela
- School of Chemical and Environmental Engineering, Technical University of Crete, 73100 Chania, Greece
| | - Antonios Kioukis
- Department of Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, 71500 Heraklion, Greece
| | - Mohsen Pourjam
- ZIEL Institute of Food and Health, Technical University of Munich, 85354 Freising, Germany
| | - Ilias Lagkouvardos
- Department of Microbiology and Microbial Pathogenesis, School of Medicine, University of Crete, 71500 Heraklion, Greece
- ZIEL Institute of Food and Health, Technical University of Munich, 85354 Freising, Germany
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71500 Heraklion, Greece
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25
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Korponai K, Szuróczki S, Márton Z, Szabó A, Morais PV, Proença DN, Tóth E, Boros E, Márialigeti K, Felföldi T. Habitat distribution of the genus Belliella in continental waters and the description of Belliella alkalica sp. nov., Belliella calami sp. nov. and Belliella filtrata sp. nov. Int J Syst Evol Microbiol 2023; 73. [PMID: 37326610 DOI: 10.1099/ijsem.0.005928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023] Open
Abstract
The genus Belliella belongs to the family Cyclobacteriaceae (order Cytophagales, phylum Bacteroidota) and harbours aerobic chemoheterotrophic bacteria. Members of this genus were isolated from various aquatic habitats, and our analysis based on global amplicon sequencing data revealed that their relative abundance can reach up to 5-10 % of the bacterioplankton in soda lakes and pans. Although a remarkable fraction of the most frequent genotypes that we identified from continental aquatic habitats is still uncultured, five new alkaliphilic Belliella strains were characterized in detail in this study, which were isolated from three different soda lakes and pans of the Carpathian Basin (Hungary). Cells of all strains were Gram-stain-negative, obligate aerobic, rod-shaped, non-motile and non-spore-forming. The isolates were oxidase- and catalase-positive, red-coloured, but did not contain flexirubin-type pigments; they formed bright red colonies that were circular, smooth and convex. Their major isoprenoid quinone was MK-7 and the predominant fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 containing C16 : 1 ω6c and/or C16 : 1 ω7c. The polar lipid profiles contained phosphatidylethanolamine, an unidentified aminophospholipid, an unidentified glycolipid, and several unidentified lipids and aminolipids. Based on whole-genome sequences, the DNA G+C content was 37.0, 37.1 and 37.8 mol % for strains R4-6T, DMA-N-10aT and U6F3T, respectively. The distinction of three new species was confirmed by in silico genomic comparison. Orthologous average nucleotide identity (<85.4 %) and digital DNA-DNA hybridization values (<38.9 %) supported phenotypic, chemotaxonomic and 16S rRNA gene sequence data and, therefore, the following three novel species are proposed: Belliella alkalica sp. nov. (represented by strains R4-6T=DSM 111903T=JCM 34281T=UCCCB122T and S4-10), Belliella calami sp. nov. (DMA-N-10aT=DSM 107340T=JCM 34280T=UCCCB121T) and Belliella filtrata sp. nov. (U6F3T=DSM 111904T=JCM 34282T=UCCCB123T and U6F1). Emended descriptions of species Belliella aquatica, Belliella baltica, Belliella buryatensis, Belliella kenyensis and Belliella pelovolcani are also presented.
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Affiliation(s)
- Kristóf Korponai
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Agricultural Institute, Centre for Agricultural Research, Brunszvik utca 2, 2462 Martonvásár, Hungary
| | - Sára Szuróczki
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Zsuzsanna Márton
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
| | - Attila Szabó
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Lennart Hjelms Vag 9, 750 07 Uppsala, Sweden
| | - Paula V Morais
- Department of Life Sciences, Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Diogo Neves Proença
- Department of Life Sciences, Centre for Mechanical Engineering, Materials and Processes, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Erika Tóth
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Emil Boros
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
| | - Károly Márialigeti
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
| | - Tamás Felföldi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary
- Institute of Aquatic Ecology, Centre for Ecological Research, Karolina út 29, 1113 Budapest, Hungary
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Wang Y, Cai X, Hu S, Qin S, Wang Z, Cao Y, Hou C, Yang J, Zhou W. Comparative genomic analysis provides insight into the phylogeny and potential mechanisms of adaptive evolution of Sphingobacterium sp. CZ-2. Gene 2023; 855:147118. [PMID: 36521669 DOI: 10.1016/j.gene.2022.147118] [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: 07/13/2022] [Revised: 11/21/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022]
Abstract
Sphingobacterium is a class of Gram-negative, non-fermentative bacilli that have received widespread attention due to their broad ecological distribution and oil degradation ability, but are rarely involved in infections. In this manuscript, a novel Sphingobacterium strain isolated from wildfire-infected tobacco leaves was named Sphingobacterium sp. CZ-2. NGS and TGS sequencing results showed a whole genome of 3.92 Mb with 40.68 mol% GC content and containing 3,462 protein-coding genes, 9 rRNA-coding genes and 50 tRNA-coding genes. Phylogenetic analysis, ANI and dDDH calculations all supported that Sphingobacterium sp. CZ-2 represented a novel species of the genus Sphingobacterium. Analysis of the specific genes of Sphingobacterium sp. CZ-2 by comparative genomics revealed that metal transport proteins encoded by the troD and cusA genes could maintain the balance of heavy metal ion concentrations in the internal environment of bacteria and avoid heavy metal toxicity while meeting the needs of growth and reproduction, and transport proteins encoded by the malG gene could keep nutrients required for the survival of bacteria. Synteny and genome evolutionary analyses of Sphingobacterium strains implicated that the gene family contraction as a major process in genome evolution, with insertional sequences leading to mutations, deletions and reversals of genes that help bacteria to withstand complex environmental changes. Complete genome sequencing and systematic comparative genomic analysis will contribute new insights into the adaptive evolution of this novel species and the genus Sphingobacterium.
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Affiliation(s)
- Yongqiang Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Xunhui Cai
- School of Electronic Information and Communications, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Shengnan Hu
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Sidong Qin
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Ziqi Wang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Yixiang Cao
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Chaoliang Hou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Jiangshan Yang
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China
| | - Wei Zhou
- Hunan Provincial Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-Making, Hunan Agricultural University, Changsha 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha 410128, China.
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27
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Gupta RK, Singh AK, Bajaj A, Khardenavis AA, Purohit HJ. Phylogenomic analysis of Citrobacter sp. strain AAK_AS5 and its metabolic capabilities to support nitrogen removal behavior. J Basic Microbiol 2023; 63:359-376. [PMID: 36453555 DOI: 10.1002/jobm.202200323] [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: 06/03/2022] [Revised: 09/02/2022] [Accepted: 10/22/2022] [Indexed: 12/03/2022]
Abstract
Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60T . Results were consistent with a digital DNA-DNA hybridization value of 80% with C. portucalensis A60T which was greater than the species boundary value >70% for delineating closely related bacterial species. Gene mining through Kyoto Encyclopedia of Genes and Genomes (KEGG), and annotation using rapid annotation subsystem technology (RAST) revealed the notable gene contents for nitrogen metabolism and other pathways associated with nitrate/nitrite ammonification (28 genes), ammonia assimilation (22 genes), and denitrification pathways (14 genes). Furthermore, the strain AAK_AS5 also exhibited a high soluble chemical oxygen demand (sCOD), NH4 + -N, and NO3 - -N removal efficiency of 91.4%, 90%, and 93.6%, respectively thus validating its genetic capability for utilizing both (NH4 )2 SO4 and KNO3 as the nitrogen source. The study provided deeper insights into the phylogenomics and the genetic potential of Citrobacter, sp. strain AAK AS5 associated with nitrogen metabolism thus signifying the potential application of the isolate for treating nitrogen-rich wastewaters.
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Affiliation(s)
- Rakesh K Gupta
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Ashish K Singh
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Abhay Bajaj
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Anshuman A Khardenavis
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Hemant J Purohit
- Environmental Biotechnology and Genomics Division (EBGD), CSIR-National Environmental Engineering Research Institute (NEERI), Nagpur, India
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28
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Mori T, Masuzawa N, Kondo K, Nakanishi Y, Chida S, Uehara D, Katahira M, Takeda M. A heterodimeric hyaluronate lyase secreted by the activated sludge bacterium Haliscomenobacter hydrossis. Biosci Biotechnol Biochem 2023; 87:256-266. [PMID: 36535637 DOI: 10.1093/bbb/zbac207] [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: 09/28/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
Haliscomenobacter hydrossis is a filamentous bacterium common in activated sludge. The bacterium was found to utilize hyaluronic acid, and hyaluronate lyase activity was detected in its culture. However, no hyaluronate lyase gene was found in the genome, suggesting the bacterium secretes a novel hyaluronate lyase. The purified enzyme exhibited two bands on SDS-PAGE and a single peak on gel filtration chromatography, suggesting a heterodimeric composition. N-terminal amino acid sequence and mass spectrometric analyses suggested that the subunits are molybdopterin-binding and [2Fe-2S]-binding subunits of a xanthine oxidase family protein. The presence of the cofactors was confirmed using spectrometric analysis. Oxidase activity was not detected, revealing that the enzyme is not an oxidase but a hyaluronate lyase. Nuclear magnetic resonance analysis of the enzymatic digest revealed that the enzyme breaks hyaluronic acid to 3-(4-deoxy-β-d-gluc-4-enuronosyl)-N-acetyl-d-glucosamine. As hyaluronate lyases (EC 4.2.2.1) are monomeric or trimeric, the enzyme is the first heterodimeric hyaluronate lyase.
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Affiliation(s)
- Tomomi Mori
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Nozomi Masuzawa
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Keiko Kondo
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Yuta Nakanishi
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Shun Chida
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Daiki Uehara
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
| | - Masato Katahira
- Institute of Advanced Energy, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Biomass Product Tree Industry-Academia Collaborative Research Laboratory, Kyoto University, Gokasho, Uji, Kyoto, Japan.,Graduate School of Energy Science, Kyoto University, Gokasho, Uji, Kyoto, Japan
| | - Minoru Takeda
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai, Hodogaya, Yokohama, Japan
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29
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Chen JW, Shih CJ, Wu LW, Wu YC, Chiang WF, Chen YL, Wu JH. Phocaeicola oris sp. nov., an anaerobic bacterium isolated from the saliva of a patient with oral squamous cell carcinoma. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749694 DOI: 10.1099/ijsem.0.005703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
A Gram-stain-negative or -positive, strictly anaerobic, non-spore-forming and pleomorphic bacterium (designated 14-104T) was isolated from the saliva sample of a patient with oral squamous cell carcinoma. It was an acid-tolerant neutralophilic mesophile, growing at between 20 and 40 °C (with optimum growth at 30 °C) and pH between pH 3.0 and 7.0 (with optimum growth at pH 6.0-7.0). It contained anteiso-C15 : 0 and C15 : 0 as the major fatty acids. The genome size of strain 14-104T was 2.98 Mbp, and the G+C content was 39.6 mol%. It shared <87 % 16S rRNA sequence similarity, <71 % orthologous average nucleotide identity, <76 % average amino acid identity and <68 %% of conserved proteins with its closest relative, Phocaeicola abscessus CCUG 55929T. Reconstruction of phylogenetic and phylogenomic trees revealed that strain 14-104T and P. abscessus CCUG 55929T were clustered as a distinct clade without any other terminal node. The phylogenetic and phylogenomic analyses along with physiological and chemotaxonomic data indicated that strain 14-104T represents a novel species in the genus Phocaeicola, for which the name Phocaeicola oris sp. nov. is proposed. The type strain is 14-104T (=BCRC 81305T= NBRC 115041T).
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Affiliation(s)
- Jiung-Wen Chen
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC.,Present address: Department of Biology, The University of Alabama at Birmingham, 1300 University Blvd, AL 35294, Birmingham, USA
| | - Chao-Jen Shih
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Li-Wha Wu
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC.,Department of Laboratory Science and Technology, College of Health Sciences, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, ROC
| | - Yen-Chi Wu
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Wei-Fan Chiang
- Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan, ROC
| | - Yuh-Ling Chen
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan, ROC
| | - Jer-Horng Wu
- Department of Environmental Engineering, National Cheng Kung University, Tainan, Taiwan, ROC
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30
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Göker M, Oren A. Proposal to include the categories kingdom and domain in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2023; 73. [PMID: 36749690 DOI: 10.1099/ijsem.0.005650] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Observations made after introduction of the phylum category into the International Code of Nomenclature of Prokaryotes (ICNP) indicate that the addition of a category should usually be conducted before informal names at that rank become widely used. It is thus investigated whether it would be beneficial to add further categories. An extrapolation from the number of names validly published under the ICNP at the distinct principal categories was conducted. This extrapolation indicated that two principal ranks above phylum rank would also harbour validly published names if the according categories were covered by the ICNP. The appropriate categories would be kingdom and domain, regarded as separate principal ranks. The benefit from introducing these ranks is confirmed by analysing the previous taxonomic activity above phylum level and the nomenclatural problems associated with this activity. An etymological examination of the way names of taxa above genus level are formed under distinct codes of nomenclature provides hints for implementing additional categories. According emendations of the ICNP are proposed to include kingdom and domain as a means of further stabilizing prokaryotic nomenclature.
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Affiliation(s)
- Markus Göker
- Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Inhoffenstrasse 7B, D-38124 Braunschweig, Germany
| | - Aharon Oren
- The Hebrew University of Jerusalem, The Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, 9190401 Jerusalem, Israel
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31
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Hellequin E, Collin S, Seder-Colomina M, Véquaud P, Anquetil C, Kish A, Huguet A. Membrane lipid adaptation of soil Bacteroidetes isolates to temperature and pH. Front Microbiol 2023; 14:1032032. [PMID: 36950164 PMCID: PMC10025309 DOI: 10.3389/fmicb.2023.1032032] [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: 08/30/2022] [Accepted: 02/15/2023] [Indexed: 03/08/2023] Open
Abstract
3-hydroxy fatty acids (3-OH FAs) are characteristic components of the Gram-negative bacterial membrane, recently proposed as promising temperature and pH (paleo) proxies in soil. Nevertheless, to date, the relationships between the 3-OH FA distribution and temperature/pH are only based on empirical studies, with no ground truthing work at the microbial level. This work investigated the influence of growth temperature and pH on the lipid composition of three strains of soil Gram-negative bacteria belonging to the Bacteroidetes phylum. Even though non-hydroxy FAs were more abundant than 3-OH FAs in the investigated strains, our results suggest that 3-OH FAs are involved in the membrane adaptation of these bacteria to temperature. The strains shared a common adaptation mechanism to temperature, with a significant increase in the ratio of anteiso vs. iso or normal 3-OH FAs at lower temperature. In contrast with temperature, no common adaptation mechanism to pH was observed, as the variations in the FA lipid profiles differed from one strain to another. We suggest that models reconstructing environmental changes in soils should include the whole suite of 3-OH FAs present in the membrane of Gram-negative bacteria, as all of them could be influenced by temperature or pH at the microbial level.
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Affiliation(s)
- Eve Hellequin
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
- *Correspondence: Eve Hellequin,
| | - Sylvie Collin
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
| | | | - Pierre Véquaud
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
| | | | - Adrienne Kish
- Muséum National d'Histoire naturelle, CNRS, Unité Molécules de Communication et Adaptation des Microorganismes UMR7245 MCAM, Paris, France
| | - Arnaud Huguet
- Sorbonne Université, CNRS, EPHE, PSL, UMR METIS, Paris, France
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32
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Kim M, Kim YS, Cha CJ. Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea. J Microbiol 2023; 61:37-47. [PMID: 36723793 DOI: 10.1007/s12275-022-00008-2] [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: 09/28/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 02/02/2023]
Abstract
Two novel bacterial species CJ51T and CJ63T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rod-shaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30 °C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51T and CJ63T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51T and CJ63T with its closely related type strains Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51T and CJ63T were iso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51T and CJ63T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51T and CJ63T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51T (= KACC 22749T = JCM 35632T) and CJ63T (= KACC 22750T = JCM 35633T).
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Affiliation(s)
- Miryung Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Yong-Seok Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Chang-Jun Cha
- Department of Systems Biotechnology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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33
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Rasmussen KL, Stamps BW, Vanzin GF, Ulrich SM, Spear JR. Spatial and temporal dynamics at an actively silicifying hydrothermal system. Front Microbiol 2023; 14:1172798. [PMID: 37206339 PMCID: PMC10188993 DOI: 10.3389/fmicb.2023.1172798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.
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Affiliation(s)
- Kalen L. Rasmussen
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | - Blake W. Stamps
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, OH, United States
| | - Gary F. Vanzin
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
| | | | - John R. Spear
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States
- *Correspondence: John R. Spear,
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34
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Shagaleeva OY, Kashatnikova DA, Kardonsky DA, Konanov DN, Efimov BA, Bagrov DV, Evtushenko EG, Chaplin AV, Silantiev AS, Filatova JV, Kolesnikova IV, Vanyushkina AA, Stimpson J, Zakharzhevskaya NB. Investigating volatile compounds in the Bacteroides secretome. Front Microbiol 2023; 14:1164877. [PMID: 37206326 PMCID: PMC10189065 DOI: 10.3389/fmicb.2023.1164877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Microorganisms and their hosts communicate with each other by secreting numerous components. This cross-kingdom cell-to-cell signaling involves proteins and small molecules, such as metabolites. These compounds can be secreted across the membrane via numerous transporters and may also be packaged in outer membrane vesicles (OMVs). Among the secreted components, volatile compounds (VOCs) are of particular interest, including butyrate and propionate, which have proven effects on intestinal, immune, and stem cells. Besides short fatty acids, other groups of volatile compounds can be either freely secreted or contained in OMVs. As vesicles might extend their activity far beyond the gastrointestinal tract, study of their cargo, including VOCs, is even more pertinent. This paper is devoted to the VOCs secretome of the Bacteroides genus. Although these bacteria are highly presented in the intestinal microbiota and are known to influence human physiology, their volatile secretome has been studied relatively poorly. The 16 most well-represented Bacteroides species were cultivated; their OMVs were isolated and characterized by NTA and TEM to determine particle morphology and their concentration. In order to analyze the VOCs secretome, we propose a headspace extraction with GC-MS analysis as a new tool for sample preparation and analysis of volatile compounds in culture media and isolated bacterial OMVs. A wide range of released VOCs, both previously characterized and newly described, have been revealed in media after cultivation. We identified more than 60 components of the volatile metabolome in bacterial media, including fatty acids, amino acids, and phenol derivatives, aldehydes and other components. We found active butyrate and indol producers among the analyzed Bacteroides species. For a number of Bacteroides species, OMVs have been isolated and characterized here for the first time as well as volatile compounds analysis in OMVs. We observed a completely different distribution of VOC in vesicles compared to the bacterial media for all analyzed Bacteroides species, including almost complete absence of fatty acids in vesicles. This article provides a comprehensive analysis of the VOCs secreted by Bacteroides species and explores new perspectives in the study of bacterial secretomes in relation the intercellular communication.
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Affiliation(s)
- Olga Yu Shagaleeva
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Daria A. Kashatnikova
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry A. Kardonsky
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry N. Konanov
- Laboratory of Mathematical Biology and Bioinformatics of Scientific Research Institute for Systems Biology and Medicine, Moscow, Russia
| | - Boris A. Efimov
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry V. Bagrov
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Andrei V. Chaplin
- Department of Microbiology and Virology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Artemiy S. Silantiev
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Julia V. Filatova
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Irina V. Kolesnikova
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Anna A. Vanyushkina
- Vladimir Zelman Center for Neurobiology and Brain Rehabilitation, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Joanna Stimpson
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Natalya B. Zakharzhevskaya
- Laboratory of Molecular Pathophysiology, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
- *Correspondence: Natalya B. Zakharzhevskaya,
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35
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Montero-Calasanz MDC, Yaramis A, Rohde M, Schumann P, Klenk HP, Meier-Kolthoff JP. Genotype-phenotype correlations within the Geodermatophilaceae. Front Microbiol 2022; 13:975365. [PMID: 36439792 PMCID: PMC9686282 DOI: 10.3389/fmicb.2022.975365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/11/2022] [Indexed: 11/11/2022] Open
Abstract
The integration of genomic information into microbial systematics along with physiological and chemotaxonomic parameters provides for a reliable classification of prokaryotes. In silico analysis of chemotaxonomic traits is now being introduced to replace characteristics traditionally determined in the laboratory with the dual goal of both increasing the speed of the description of taxa and the accuracy and consistency of taxonomic reports. Genomics has already successfully been applied in the taxonomic rearrangement of Geodermatophilaceae (Actinomycetota) but in the light of new genomic data the taxonomy of the family needs to be revisited. In conjunction with the taxonomic characterisation of four strains phylogenetically located within the family, we conducted a phylogenetic analysis of the whole proteomes of the sequenced type strains and established genotype-phenotype correlations for traits related to chemotaxonomy, cell morphology and metabolism. Results indicated that the four isolates under study represent four novel species within the genus Blastococcus. Additionally, the genera Blastococcus, Geodermatophilus and Modestobacter were shown to be paraphyletic. Consequently, the new genera Trujillonella, Pleomorpha and Goekera were proposed within the Geodermatophilaceae and Blastococcus endophyticus was reclassified as Trujillonella endophytica comb. nov., Geodermatophilus daqingensis as Pleomorpha daqingensis comb. nov. and Modestobacter deserti as Goekera deserti comb. nov. Accordingly, we also proposed emended descriptions of Blastococcus aggregatus, Blastococcus jejuensis, Blastococcus saxobsidens and Blastococcus xanthilyniticus. In silico chemotaxonomic results were overall consistent with wet-lab results. Even though in silico discriminatory levels varied depending on the respective chemotaxonomic trait, this approach is promising for effectively replacing and/or complementing chemotaxonomic analyses at taxonomic ranks above the species level. Finally, interesting but previously overlooked insights regarding morphology and ecology were revealed by the presence of a repertoire of genes related to flagellum synthesis, chemotaxis, spore production and pilus assembly in all representatives of the family. A rich carbon metabolism including four different CO2 fixation pathways and a battery of enzymes able to degrade complex carbohydrates were also identified in Blastococcus genomes.
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Affiliation(s)
- Maria del Carmen Montero-Calasanz
- IFAPA Las Torres-Andalusian Institute of Agricultural and Fisheries Research and Training, Junta de Andalucía, Seville, Spain,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom,*Correspondence: Maria del Carmen Montero-Calasanz,
| | - Adnan Yaramis
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Manfred Rohde
- Central Facility for Microscopy, HZI – Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Hans-Peter Klenk
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Jan P. Meier-Kolthoff
- Department Bioinformatics and Databases, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Wang Q, Zhang L, Zhang Y, Chen H, Song J, Lyu M, Chen R, Zhang L. Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7. Front Microbiol 2022; 13:1008648. [PMID: 36419435 PMCID: PMC9677121 DOI: 10.3389/fmicb.2022.1008648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/10/2022] [Indexed: 11/09/2022] Open
Abstract
Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.
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Affiliation(s)
- Qian Wang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lei Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Yiju Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
| | - Huamin Chen
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianghua Song
- College of Horticulture, Anhui Agricultural University, Hefei, China
| | - Mingjie Lyu
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Rui Chen
- Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Lixin Zhang
- Anhui Province Key Laboratory of Integrated Pest Management on Crops, College of Plant Protection, Anhui Agricultural University, Hefei, China
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Lixin Zhang,
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Huang Z, Hong Q, Lai Q, Zhang Q. Portibacter marinus sp. nov., isolated from the sediment on the surface of plastics and proposal of a novel genus Neolewinella gen. nov. based on the genome-based phylogeny of the family Lewinellaceae. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A Gram-stain-negative, rod-shaped and orange-pigmented bacterial strain designated 10MBP4-2-1T was isolated from the sediment on the surface of a plastic straw collected from oyster-farming areas in Quanzhou Bay, PR China. Catalase activity and oxidase activity were positive. Flexirubin-type pigment was absent. The 16S rRNA gene of strain 10MBP4-2-1T showed highest sequence similarity to
Portibacter lacus
YM8-076T of 98.3 %. Phylogenetic analysis based on 16S rRNA gene sequences and 120 conserved concatenated proteins indicated that strain 10MBP4-2-1T was affiliated to the genus
Portibacter
and formed a monophyletic clade with
P. lacus
YM8-076T. The digital DNA–DNA hybridization, average nucleotide identity and average amino acid identity values between strain 10MBP4-2-1T and
P. lacus
YM8-076T were estimated to be 17.7, 70.4 and 70.3 %, respectively. The respiratory quinone was menaquinone 7. The major fatty acid composition was iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c). The draft genome size was 5 191 941 bp with DNA G+C content of 39.2 %. Based on phylogenetic analyses and whole genomic comparisons, strain 10MBP4-2-1T represents a novel species, for which the name Portibacter marinus sp. nov. is proposed. The type strain is 10MBP4-2-1T (=MCCC 1K07073T=KCTC 92101T). Additionally, phylogeny and whole genomic comparison of the family
Lewinellaceae
placed
Lewinella cohaerens
and the remaining
Lewinella
(currently comprising 11 species) in two clearly distinguishable clades recognized at the genus level. Thus, a novel genus named Neolewinella gen. nov. is proposed to accommodate the 11 species. Our study provides a taxonomic framework for the family
Lewinellaceae
based on genomic data.
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Affiliation(s)
- Zhaobin Huang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China
- Fujian Province Key Laboratory for the Development of Bioactive Material from Marine Algae, Quanzhou, PR China
| | - Qianling Hong
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China
| | - Qiliang Lai
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, PR China
| | - Qiufang Zhang
- College of Oceanology and Food Science, Quanzhou Normal University, Quanzhou, PR China
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A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter. Syst Appl Microbiol 2022; 45:126354. [DOI: 10.1016/j.syapm.2022.126354] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 06/24/2022] [Accepted: 08/15/2022] [Indexed: 11/19/2022]
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Advanced prokaryotic systematics: the modern face of an ancient science. New Microbes New Infect 2022; 49-50:101036. [DOI: 10.1016/j.nmni.2022.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/13/2022] Open
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Liu X, Wang D, Yin Z, Sun L, Pang S, Liu J, Li W, Cui S, Huang W, Du Y, Xie Z. Insights into Evolutionary, Genomic, and Biogeographic Characterizations of Chryseobacterium nepalense Represented by a Polyvinyl Alcohol-Degrading Bacterium, AC3. Microbiol Spectr 2022; 10:e0217922. [PMID: 36000867 PMCID: PMC9602593 DOI: 10.1128/spectrum.02179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 12/31/2022] Open
Abstract
Chryseobacterium spp. are Gram-negative rods found ubiquitously in the environment, with certain species being reported as having unusual degrading properties. Polyvinyl alcohol (PVA) is used widely in industry but causes serious global environmental pollution. Here, we report the complete genome sequence of a novel bacterium, AC3, that efficiently degrades PVA. As the representative genome of Chryseobacterium nepalense, key genomic characteristics (e.g., mobile genetic elements, horizontal genes, genome-scale metabolic network, secondary metabolite biosynthesis gene clusters, and carbohydrate-active enzymes) were comprehensively investigated to reveal the potential genetic features of this species. Core genome phylogenetic analysis in combination with average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization values provided an accurate taxonomic position of C. nepalense in the genus Chryseobacterium. Comparative genomic analysis of AC3 with closely related species suggested evolutionary dynamics characterized by a species-specific genetic repertoire, dramatic rearrangements, and evolutionary constraints driven by selective pressure, which facilitated the speciation and adaptative evolution of C. nepalense. Biogeographic characterization indicated that this species is ubiquitously distributed not only in soil habitats but also in a variety of other source niches. Bioinformatic analysis revealed the potential genetic basis of PVA degradation in AC3, which included six putative genes associated with the synthesis of PVA dehydrogenase, cytochrome c, oxidized PVA hydrolase, and secondary alcohol dehydrogenase. Our study reports the first complete genome of C. nepalense with PVA-degrading properties, providing comprehensive insights into the genomic characteristics of this species and increasing our understanding of the microbial degradation of PVA. IMPORTANCE Although PVA is a biodegradable polymer, the widespread use of PVA in global industrialization has resulted in serious environmental problems. To date, knowledge of effective and applicable PVA-degrading bacteria is limited, and thus, the discovery of novel PVA biodegraders is pertinent. Here, we isolated a novel bacterial strain, AC3, which efficiently degraded PVA. The complete genome of AC3 was sequenced as the first genome sequence of the species C. nepalense. Comparative genomic analysis was performed to comprehensively investigate the phylogenetic relationships, genome-scale metabolic network, key genomic characteristics associated with genomic evolution, evolutionary dynamics between AC3 and its close relatives, and biogeographic characterization of C. nepalense, particularly regarding the potential genetic basis of PVA degradation. These findings could advance our understanding of the genomic characteristics of C. nepalense and PVA bioremediation.
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Affiliation(s)
- Xinbei Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Dandan Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Li Sun
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Shiqi Pang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Jianing Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Wei Li
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, People’s Republic of China
| | - Shiyu Cui
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Weiwei Huang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Yuhui Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
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Alam K, Hao J, Zhong L, Fan G, Ouyang Q, Islam MM, Islam S, Sun H, Zhang Y, Li R, Li A. Complete genome sequencing and in silico genome mining reveal the promising metabolic potential in Streptomyces strain CS-7. Front Microbiol 2022; 13:939919. [PMID: 36274688 PMCID: PMC9581153 DOI: 10.3389/fmicb.2022.939919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Gram-positive Streptomyces bacteria can produce valuable secondary metabolites. Streptomyces genomes include huge unknown silent natural product (NP) biosynthetic gene clusters (BGCs), making them a potential drug discovery repository. To collect antibiotic-producing bacteria from unexplored areas, we identified Streptomyces sp. CS-7 from mountain soil samples in Changsha, P.R. China, which showed strong antibacterial activity. Complete genome sequencing and prediction in silico revealed that its 8.4 Mbp genome contains a total of 36 BGCs for NPs. We purified two important antibiotics from this strain, which were structurally elucidated to be mayamycin and mayamycin B active against Staphylococcus aureus. We identified functionally a BGC for the biosynthesis of these two compounds by BGC direct cloning and heterologous expression in Streptomyces albus. The data here supported this Streptomyces species, especially from unexplored habitats, having a high potential for new NPs.
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Affiliation(s)
- Khorshed Alam
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Jinfang Hao
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Lin Zhong
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guoqing Fan
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qing Ouyang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Md. Mahmudul Islam
- Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affiliated University of Rajshahi, Rajshahi, Bangladesh
| | - Saiful Islam
- Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram Laboratories, Chattogram, Bangladesh
| | - Hongluan Sun
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Chinese Academy of Sciences, Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China
| | - Ruijuan Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Ruijuan Li,
| | - Aiying Li
- Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Aiying Li,
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42
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Hudson J, Egan S. Opportunistic diseases in marine eukaryotes: Could Bacteroidota be the next threat to ocean life? Environ Microbiol 2022; 24:4505-4518. [PMID: 35706128 PMCID: PMC9804302 DOI: 10.1111/1462-2920.16094] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 01/05/2023]
Abstract
Bacteria within the phylum Bacteroidota (Bacteroidetes) are known to cause devastating and widespread disease outbreaks in marine eukaryotic hosts. However, with few pathogens described in detail, their prevalence and virulence strategies remain largely unknown. Here, we systematically reviewed the literature to evaluate the current understanding of Bacteroidota that cause disease in marine hosts. Isolates affiliated with the genera Tenacibaculum and Aquimarina (Flavobacteriaceae) were the most widely reported and characterized pathogens. Although cultured isolates were predominantly Flavobacteriia, culture-independent studies also found classes Bacteroidia, Cytophagia and Sphingobacteriia associated with disease. We found that pathogenic marine Bacteroidota largely conformed to an opportunistic lifestyle but could also act as secondary pathogens or were involved in polymicrobial diseases. Many diseases were also associated with an environmental stressor, especially those affecting coral, macroalgae and fish. Key virulence traits included the production of adhesins and host tissue-degrading enzymes. Overall, the nature of disease involving Bacteroidota pathogens appears to be an outcome of complex host-pathogen-environment interactions; however, our understanding of virulence remains limited by the lack of functional characterization studies. This is concerning as Bacteroidota have the potential to emerge as a serious threat to marine ecosystems and aquaculture industries, driven by global changes in ocean conditions.
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Affiliation(s)
- Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental SciencesThe University of New South WalesSydneyAustralia
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43
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Whitman WB, Chuvochina M, Hedlund BP, Hugenholtz P, Konstantinidis KT, Murray AE, Palmer M, Parks DH, Probst AJ, Reysenbach AL, Rodriguez-R LM, Rossello-Mora R, Sutcliffe I, Venter SN. Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type. Syst Appl Microbiol 2022; 45:126305. [PMID: 36049255 PMCID: PMC9489671 DOI: 10.1016/j.syapm.2022.126305] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 01/30/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022]
Abstract
Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.
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Affiliation(s)
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Brian P Hedlund
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | | | - Alison E Murray
- Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, USA
| | - Marike Palmer
- School of Life Sciences, University of Nevada, Las Vegas, NV, USA
| | - Donovan H Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, Australia
| | - Alexander J Probst
- Department of Chemistry, Environmental Microbiology and Biotechnology (EMB), Group for Aquatic Microbial Ecology and Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | | | - Luis M Rodriguez-R
- Department of Microbiology and Digital Science Center (DiSC), University of Innsbruck, Innrain 15 / 01-05, Innsbruck 6020, Austria
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (CSIC-UIB), Esporles, Illes Balears, Spain
| | - Iain Sutcliffe
- Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Kondrotaite Z, Valk LC, Petriglieri F, Singleton C, Nierychlo M, Dueholm MKD, Nielsen PH. Diversity and Ecophysiology of the Genus OLB8 and Other Abundant Uncultured Saprospiraceae Genera in Global Wastewater Treatment Systems. Front Microbiol 2022; 13:917553. [PMID: 35875537 PMCID: PMC9304909 DOI: 10.3389/fmicb.2022.917553] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
The Saprospiraceae family within the phylum Bacteroidota is commonly present and highly abundant in wastewater treatment plants (WWTPs) worldwide, but little is known about its role. In this study, we used MiDAS 4 global survey with samples from 30 countries to analyze the abundance and distribution of members of Saprospiraceae. Phylogenomics were used to delineate five new genera from a set of 31 high-quality metagenome-assembled genomes from Danish WWTPs. Newly designed probes for fluorescence in situ hybridization (FISH) revealed rod-shaped morphologies for all genera analyzed, including OLB8, present mostly inside the activated sludge flocs. The genomes revealed potential metabolic capabilities for the degradation of polysaccharides, proteins, and other complex molecules; partial denitrification; and storage of intracellular polymers (glycogen, polyphosphate, and polyhydroxyalkanoates). FISH in combination with Raman microspectroscopy confirmed the presence of intracellular glycogen in Candidatus Brachybacter, Candidatus Parvibacillus calidus (both from the former genus OLB8), and Candidatus Opimibacter, and the presence of polyhydroxyalkanoates in Candidatus Defluviibacterium haderslevense and Candidatus Vicinibacter. These results provide the first overview of the most abundant novel Saprospiraceae genera present in WWTPs across the world and their potential involvement in nutrient removal and the degradation of macromolecules.
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Affiliation(s)
| | | | | | | | | | | | - Per H. Nielsen
- Department of Chemistry and Bioscience, Center of Microbial Communities, Aalborg University, Aalborg, Denmark
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45
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Brinkmann S, Kurz M, Patras MA, Hartwig C, Marner M, Leis B, Billion A, Kleiner Y, Bauer A, Toti L, Pöverlein C, Hammann PE, Vilcinskas A, Glaeser J, Spohn M, Schäberle TF. Genomic and Chemical Decryption of the Bacteroidetes Phylum for Its Potential to Biosynthesize Natural Products. Microbiol Spectr 2022; 10:e0247921. [PMID: 35442080 PMCID: PMC9248904 DOI: 10.1128/spectrum.02479-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 03/29/2022] [Indexed: 12/04/2022] Open
Abstract
With progress in genome sequencing and data sharing, 1,000s of bacterial genomes are publicly available. Genome mining-using bioinformatics tools in terms of biosynthetic gene cluster (BGC) identification, analysis, and rating-has become a key technology to explore the capabilities for natural product (NP) biosynthesis. Comprehensively, analyzing the genetic potential of the phylum Bacteroidetes revealed Chitinophaga as the most talented genus in terms of BGC abundance and diversity. Guided by the computational predictions, we conducted a metabolomics and bioactivity driven NP discovery program on 25 Chitinophaga strains. High numbers of strain-specific metabolite buckets confirmed the upfront predicted biosynthetic potential and revealed a tremendous uncharted chemical space. Mining this data set, we isolated the new iron chelating nonribosomally synthesized cyclic tetradeca- and pentadecalipodepsipeptide antibiotics chitinopeptins with activity against Candida, produced by C. eiseniae DSM 22224 and C. flava KCTC 62435, respectively. IMPORTANCE The development of pipelines for anti-infectives to be applied in plant, animal, and human health management are dried up. However, the resistance development against compounds in use calls for new lead structures. To fill this gap and to enhance the probability of success for the discovery of new bioactive natural products, microbial taxa currently underinvestigated must be mined. This study investigates the potential within the bacterial phylum Bacteroidetes. A combination of omics-technologies revealed taxonomical hot spots for specialized metabolites. Genome- and metabolome-based analyses showed that the phylum covers a new chemical space compared with classic natural product producers. Members of the Bacteroidetes may thus present a promising bioresource for future screening and isolation campaigns.
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Affiliation(s)
- Stephan Brinkmann
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Michael Kurz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Maria A. Patras
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Christoph Hartwig
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Michael Marner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Benedikt Leis
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - André Billion
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Yolanda Kleiner
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Armin Bauer
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Luigi Toti
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jens Glaeser
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Evotec International GmbH, Göttingen, Germany
| | - Marius Spohn
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
| | - Till F. Schäberle
- Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), Branch for Bioresources, Giessen, Germany
- Institute for Insect Biotechnology, Justus-Liebig-University Giessen, Giessen, Germany
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46
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Pitt A, Koll U, Schmidt J, Neumann-Schaal M, Wolf J, Krausz S, Hahn MW. Aquirufa lenticrescens sp. nov. and Aquirufa aurantiipilula sp. nov.: two new species of a lineage of widespread freshwater bacteria. Arch Microbiol 2022; 204:356. [PMID: 35654990 PMCID: PMC9163014 DOI: 10.1007/s00203-022-02950-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
Abstract
Two bacterial strains, 9H-EGSET and 15D-MOBT, were isolated from small freshwater habitats located near Salzburg, Austria. They showed the highest 16S rRNA sequence similarities of 100% and 99.9%, respectively, with type strains of species of the genus Aquirufa (Bacteroidota). Genome-based phylogenetic reconstructions with 119 amino acid sequences assigned the new taxa to the two distinct branches of the genus Aquirufa. Whole-genome average nucleotide identities were calculated with all possible pairs belonging to the genus. Values between 75.4% and 88.6% revealed that the two new strains represent each a new species. Like all, so far described members of the genus, they grew aerobically and chemoorganotrophically, were rod-shaped, red-pigmented, and motile by gliding, and showed genome sizes of about 3 Mbp and G + C values of about 40%. They could be distinguished by some phenotypic and chemotaxonomic features from their nearest related species. Until now, strain 9H-EGSET is the only one among the Aquirufa strains which contained traces of MK8 as respiratory quinone, and strain 15D-MOBT is the only one that formed tiny orange globules in liquid medium. The genome of strain 9H-EGSET comprised genes for the complete light-harvesting rhodopsin / retinal system, in the case of 15D-MOBT genes predicted for a nitrous oxide reductase were present. For the two new species of the genus Aquirufa, we propose to establish the names Aquirufa lenticrescens for strain 9H-EGSET (= JCM 34077 T = CIP 111926 T) and Aquirufa aurantiipilula for strain 15D-MOBT (= JCM 34078 T = CIP 111925 T).
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Khare D, Chandwadkar P, Acharya C. Gliding motility of a uranium-tolerant Bacteroidetes bacterium Chryseobacterium sp. strain PMSZPI: insights into the architecture of spreading colonies. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:453-463. [PMID: 34907658 DOI: 10.1111/1758-2229.13034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 10/29/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Uranium-tolerant soil bacterium Chryseobacterium sp. strain PMSZPI moved over solid agar surfaces by gliding motility thereby forming spreading colonies which is a hallmark of members of Bacteroidetes phylum. PMSZPI genome harboured orthologs of all the gld and spr genes considered as core bacteroidetes gliding motility genes of which gldK, gldL, gldM and gldN were co-transcribed. Here, we present the intriguing interplay between gliding motility and cellular organization in PMSZPI spreading colonies. While nutrient deficiency enhanced colony spreading, high agar concentrations and presence of motility inhibitor like 5-hydroxyindole reduced the spreading. A detailed in situ structural analysis of spreading colonies revealed closely packed cells forming multiple layers at centre of colony while the edges showed clusters of cells periodically arranged in hexagonal lattices interconnected with each other. The cell migration within colony was visualized as branched structures wherein the cells were buried within extracellular matrix. PMSZPI colonies exhibited strong iridescence possibly as a result of periodicity within the cell population achieved through gliding motility. Presence of uranium reduced motility and iridescence and induced biofilm formation. The coordinated study of gliding motility and iridescence apparently influenced by uranium provides unique insights into the lifestyle of PMSZPI residing in uranium enriched environment.
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Affiliation(s)
- Devanshi Khare
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Pallavi Chandwadkar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Celin Acharya
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
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Rhodoflexus caldus gen. nov., sp. nov., a new member of the phylum Bacteroidota isolated from a hot spring sediment. Antonie van Leeuwenhoek 2022; 115:889-898. [PMID: 35562517 DOI: 10.1007/s10482-022-01742-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/15/2022] [Indexed: 10/18/2022]
Abstract
A thermophilic bacterium, designated strain SYSU G04325T, was isolated from a hot spring sediment in Yunnan, China. Polyphasic taxonomic analyses and whole-genome sequencing were used to determine the taxonomic position of the strain. Phylogenetic analysis using 16S rRNA gene sequences indicated that strain SYSU G04325T shows high sequence similarity to Thermoflexibacter ruber NBRC 16677T (86.2%). The strain can be differentiated from other species of the family Thermoflexibacteraceae by its distinct phenotypic and genotypic characteristics. Cells of the strain SYSU G04325T were observed to be aerobic, Gram-stain negative and filamentous. Growth was found to occur optimally at 45 ºC and pH 7.0. In addition, the respiratory quinone was identified as menaquinone-7, while the major fatty acids (> 10%) were identified as iso-C15:0, iso-C17:0 and Summed Feature 9 (iso-C17:1ω9c). The polar lipids detected included phosphatidylethanolamine, three unidentified phospholipids, one unidentified glycolipid, five unidentified aminolipids and four unidentified polar lipids. The G + C content of the genomic DNA was determined to be 47.6% based on the draft genome sequence. On the basis of phenotypic, genotypic and phylogenetic data, strain SYSU G04325T is concluded to represent a novel species of a novel genus in the family Thermoflexibacteraceae, for which the name Rhodoflexus caldus gen. nov., sp. nov. is proposed. The type strain of Rhodoflexus caldus is SYSU G04325T (= MCCC 1K06127T = KCTC 82848T).
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Heidler von Heilborn D, Nover LL, Weber M, Hölzl G, Gisch N, Waldhans C, Mittler M, Kreyenschmidt J, Woehle C, Hüttel B, Lipski A. Polar lipid characterization and description of Chryseobacterium capnotolerans sp. nov., isolated from high CO2-containing atmosphere and emended descriptions of the genus Chryseobacterium, and the species C. balustinum, C. daecheongense, C. formosense, C. gleum, C. indologenes, C. joostei, C. scophthalmum and C. ureilyticum. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005372] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Modified atmosphere (MA) packaging plays an important role in improving food quality and safety. By using different gas mixtures and packaging materials the shelf life of fresh produce can significantly be increased. A Gram-negative-staining, rod-shaped, orange-pigmented strain DH-B6T, has been isolated from MA packed raw pork sausage (20% CO2, 80% O2). The strain produced biofilms and showed growth at high CO2 levels of up to 40%. Complete 16S rRNA gene and whole-genome sequences revealed that strain DH-B6T belongs to the genus
Chryseobacterium
, being closely related to strain
Chryseobacterium indologenes
DSM 16777T (98.4%), followed by
Chryseobacterium gleum
NCTC11432T (98.3%) and
Chryseobacterium lactis
KC1864T (98.2%). Average nucleotide identity value between DH-B6T and
C. indologenes
DSM 16777T was 81.1% and digital DNA–DNA hybridisation was 24.9%, respectively. The DNA G+C content was 35.51 mol%. Chemotaxonomical analysis revealed the presence of the rare glycine lipid cytolipin, the serine-glycine lipid flavolipin and the sulfonolipid sulfobacin A, as well as phosphatidylethanolamine, monohexosyldiacylglycerol and ornithine lipid, including the hydroxylated forms. Major fatty acids were iC15 : 0 (50.7%) and iC17 : 1 cis 9 (28.7%), followed by iC15 : 0 2-OH (7.0%) and iC17 : 0 3-OH (6.2%). The isolated strain contained MK-6 as the only respiratory quinone and flexirubin-like pigments were detected as the major pigments. Based on the phenotypic, chemotaxonomic and phylogenetic characteristics, the strain DH-B6T (=DSM 110542T=LMG 31915T) represents a novel species of the genus
Chryseobacterium
, for which the name Chryseobacterium capnotolerans sp. nov. is proposed. Emended descriptions of the genus
Chryseobacterium
and eight species of this genus based on polar lipid characterisation are also proposed.
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Affiliation(s)
- David Heidler von Heilborn
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - Lena-Luisa Nover
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - Mareike Weber
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
| | - Georg Hölzl
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Karlrobert-Kreiten-Str. 13, 53115 Bonn, Germany
| | - Nicolas Gisch
- Bioanalytical Chemistry, Research Center Borstel, Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
| | - Claudia Waldhans
- Institute of Animal Sciences, Cold-Chain Management, University of Bonn, Katzenburgweg 7-9, 53115 Bonn, Germany
| | - Maureen Mittler
- Institute of Animal Sciences, Cold-Chain Management, University of Bonn, Katzenburgweg 7-9, 53115 Bonn, Germany
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, Cold-Chain Management, University of Bonn, Katzenburgweg 7-9, 53115 Bonn, Germany
| | - Christian Woehle
- Max Planck Institute for Plant Breeding Research, Max Planck-Genome-centre Cologne (MP-GC), Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - Bruno Hüttel
- Max Planck Institute for Plant Breeding Research, Max Planck-Genome-centre Cologne (MP-GC), Carl-von-Linné-Weg 10, 50829 Cologne, Germany
| | - André Lipski
- Institute of Nutritional and Food Science, Food Microbiology and Hygiene, University of Bonn, Friedrich-Hirzebruch-Allee 7, 53115 Bonn, Germany
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Bacteremia due to Prevotella oris of probable hepatic origin. Anaerobe 2022; 76:102586. [DOI: 10.1016/j.anaerobe.2022.102586] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 12/25/2022]
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