151
|
Tóth Á, Máté R, Kutasi J, Tóth E, Bóka K, Táncsics A, Nagy I, Kovács G, Kosztik J, Bata-Vidács I, Kukolya J. Sphingobacterium hungaricum sp. nov. a novel species on the borderline of the genus Sphingobacterium. Int J Syst Evol Microbiol 2021; 71. [PMID: 34779758 DOI: 10.1099/ijsem.0.005105] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-reaction-negative bacterial strain, designated Kb22T, was isolated from agricultural soil and characterized using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (94.39 %) to Sphingobacterium nematocida M-SX103T. The highest average nucleotide identity value (71.83 %) was found with Sphingobacterium composti T5-12T, and the highest amino acid identity value (66.65 %) was found with Sphingobacterium olei HAL-9T. Cells are aerobic, non-motile rods. The isolate was found to be positive for catalase and oxidase tests. The assembled genome of strain Kb22T has a total length of 4,06 Mb, the DNA G+C content is 38.1 mol%. The only isoprenoid quinone is menaquinone 7 (MK-7). The major fatty acids are iso-C15:0 (28.4%), summed feature 3 (C16:1 ω7c and/or iso-C15:0 2-OH) (25.7 %) and iso-C17:0 3-OH (19.7 %). Based on phenotypic characteristics and phylogenetic results, it is concluded that strain Kb22T is a member of the genus Sphingobacterium and represents a novel species for which the name Sphingobacterium hungaricum sp. nov. is proposed. The type strain of the species is strain Kb22T (=LMG 31574T=NCAIM B.02638T).
Collapse
Affiliation(s)
- Ákos Tóth
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Rózsa Máté
- BioFil Microbiological, Biotechnological and Biochemical Ltd., Budapest, Hungary
| | - József Kutasi
- BioFil Microbiological, Biotechnological and Biochemical Ltd., Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary
| | - Gábor Kovács
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,University of Sopron, Sopron, Hungary
| | - Judit Kosztik
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Ildikó Bata-Vidács
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - József Kukolya
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| |
Collapse
|
152
|
Králová S, Busse HJ, Bezdíček M, Sandoval-Powers M, Nykrýnová M, Staňková E, Krsek D, Sedláček I. Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Front Microbiol 2021; 12:729977. [PMID: 34745033 PMCID: PMC8570120 DOI: 10.3389/fmicb.2021.729977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
Collapse
Affiliation(s)
- Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Matěj Bezdíček
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, Masaryk University, Brno, Czechia
| | | | - Markéta Nykrýnová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, National Institute of Public Health, Prague, Czechia
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| |
Collapse
|
153
|
Lodha T, Narvekar S, Karodi P. Classification of uncultivated anammox bacteria and Candidatus Uabimicrobium into new classes and provisional nomenclature as Candidatus Brocadiia classis nov. and Candidatus Uabimicrobiia classis nov. of the phylum Planctomycetes and novel family Candidatus Scalinduaceae fam. nov to accommodate the genus Candidatus Scalindua. Syst Appl Microbiol 2021; 44:126272. [PMID: 34735804 DOI: 10.1016/j.syapm.2021.126272] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 11/26/2022]
Abstract
The phylum Planctomycetes is metabolically unique group of bacteria divided in two classes Planctomycetia and Phycisphaerae. Anaerobic ammonia-oxidizing (anammox) bacteria are the uncultured representatives of the phylum Planctomycetes. Anammox bacterial genera are placed in the family Candidatus (Ca.) Brocadiaceae of the order Ca. Brocadiales, assigned to the class Planctomycetia. Phylogenetic analysis, showed that the anammox bacteria and Ca. Uabimicrobium form a divergent clade from the rest of the cultured representatives of the phylum Planctomycetes. The phylogenetic study, pairwise distance and Average Amino acid Identity (AAI) showed that anammox bacteria don't belong to the classes Planctomycetia and Phycisphaerae. Anammox bacteria and Ca. Uabimicrobium form a deep-branching third clade in the phylogenetic analysis indicating that it is the most ancient third class within the phylum Planctomycetes. Phenotypic characters also separate anammox bacteria from classes Planctomycetia and Phycisphaerae. Therefore, based on phenotypic, phylogenetic, pairwise distance, AAI and phylogenomic analysis we propose a novel class Ca. Brocadiia to accommodate the order Ca. Brocadiales of anammox bacteria except Ca. Anammoximicrobium. Genera Ca. Jettenia, Ca. Anammoxoglobus, Ca. Kuenenia and Ca. Brocadia show their phylogenetic affiliation to the family Ca. Brocadiaceae. However, Ca. Scalindua showed a distant relationship with the family Ca. Brocadiaceae. Therefore, we suggest the exclusion of the genus Ca. Scalindua from the family Ca. Brocadiaceae; and propose its inclusion under a novel family with a provisional name as Ca. Scalinduaceae fam. nov. Similarly, Ca. Uabimicrobium amporphum showed distinct phylogenetic affiliation, therefore we propose a novel class Ca. Uabimicrobiia classis nov. to accommodate the genus Ca. Uabimicrobium.
Collapse
Affiliation(s)
- Tushar Lodha
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India.
| | - Simran Narvekar
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
| | - Prachi Karodi
- National Centre for Microbial Resource, National Centre for Cell Science, Pune 411021, India
| |
Collapse
|
154
|
Draft Genome Sequence of Vibrio jasicida 20LP, an Opportunistic Bacterium Isolated from Fish Larvae. Microbiol Resour Announc 2021; 10:e0081321. [PMID: 34734757 PMCID: PMC8567781 DOI: 10.1128/mra.00813-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We present the genome sequence of Vibrio jasicida 20LP, a bacterial strain retrieved from larvae of gilthead seabream (Sparus aurata), a highly valuable, model fish species in land-based aquaculture. Annotation of the V. jasicida 20LP genome reveals multiple genomic features potentially underpinning opportunistic associations with diverse marine animals.
Collapse
|
155
|
Albuquerque P, Ribeiro I, Correia S, Mucha AP, Tamagnini P, Braga-Henriques A, Carvalho MDF, Mendes MV. Complete Genome Sequence of Two Deep-Sea Streptomyces Isolates from Madeira Archipelago and Evaluation of Their Biosynthetic Potential. Mar Drugs 2021; 19:md19110621. [PMID: 34822492 PMCID: PMC8622039 DOI: 10.3390/md19110621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022] Open
Abstract
The deep-sea constitutes a true unexplored frontier and a potential source of innovative drug scaffolds. Here, we present the genome sequence of two novel marine actinobacterial strains, MA3_2.13 and S07_1.15, isolated from deep-sea samples (sediments and sponge) and collected at Madeira archipelago (NE Atlantic Ocean; Portugal). The de novo assembly of both genomes was achieved using a hybrid strategy that combines short-reads (Illumina) and long-reads (PacBio) sequencing data. Phylogenetic analyses showed that strain MA3_2.13 is a new species of the Streptomyces genus, whereas strain S07_1.15 is closely related to the type strain of Streptomyces xinghaiensis. In silico analysis revealed that the total length of predicted biosynthetic gene clusters (BGCs) accounted for a high percentage of the MA3_2.13 genome, with several potential new metabolites identified. Strain S07_1.15 had, with a few exceptions, a predicted metabolic profile similar to S. xinghaiensis. In this work, we implemented a straightforward approach for generating high-quality genomes of new bacterial isolates and analyse in silico their potential to produce novel NPs. The inclusion of these in silico dereplication steps allows to minimize the rediscovery rates of traditional natural products screening methodologies and expedite the drug discovery process.
Collapse
Affiliation(s)
- Pedro Albuquerque
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Inês Ribeiro
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Sofia Correia
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
| | - Ana Paula Mucha
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Paula Tamagnini
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007 Porto, Portugal
| | - Andreia Braga-Henriques
- OOM—Oceanic Observatory of Madeira & MARE—Marine and Environmental Sciences Centre, ARDITI—Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação, Caminho da Penteada, 9020-105 Funchal, Portugal;
- Regional Directorate for Fisheries, Regional Secretariat for the Sea and Fisheries, Government of the Azores, Rua Cônsul Dabney—Colónia Alemã, 9900-014 Horta, Portugal
| | - Maria de Fátima Carvalho
- CIIMAR—Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208 Matosinhos, Portugal; (I.R.); (S.C.); (A.P.M.); (M.d.F.C.)
- ICBAS—Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Marta V. Mendes
- i3S—Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal; (P.A.); (P.T.)
- IBMC—Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen 208, 4200-135 Porto, Portugal
- Correspondence:
| |
Collapse
|
156
|
Teo WFA, Tan GYA, Li WJ. Taxonomic note on the family Pseudonocardiaceae based on phylogenomic analysis and descriptions of Allosaccharopolyspora gen. nov. and Halosaccharopolyspora gen. nov. Int J Syst Evol Microbiol 2021; 71. [PMID: 34714227 DOI: 10.1099/ijsem.0.005075] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The taxonomic positions of members within the family Pseudonocardiaceae were assessed based on phylogenomic trees reconstructed using core-proteome and genome blast distance phylogeny approaches. The closely clustered genome sequences from the type strains of validly published names within the family Pseudonocardiaceae were analysed using overall genome-related indices based on average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values. The family Pseudonocardiaceae consists of the type genus Pseudonocardia, as well as the genera Actinoalloteichus, Actinocrispum, Actinokineospora, Actinomycetospora, Actinophytocola, Actinopolyspora, Actinorectispora, Actinosynnema, Allokutzneria, Allosaccharopolyspora gen. nov., Amycolatopsis, Bounagaea, Crossiella, Gandjariella, Goodfellowiella, Haloactinomyces, Haloechinothrix, Halopolyspora, Halosaccharopolyspora gen. nov., Herbihabitans, Kibdelosporangium, Kutzneria, Labedaea, Lentzea, Longimycelium, Prauserella, Saccharomonospora, Saccharopolyspora, Saccharothrix, Salinifilum, Sciscionella, Streptoalloteichus, Tamaricihabitans, Thermocrispum, Thermotunica and Umezawaea. The G+C contents of the Pseudonocardiaceae genomes ranged from 66.2 to 74.6 mol% and genome sizes ranged from 3.69 to 12.28 Mbp. Based on the results of phylogenomic analysis, the names Allosaccharopolyspora coralli comb. nov., Halosaccharopolyspora lacisalsi comb. nov. and Actinoalloteichus caeruleus comb. nov. are proposed. This study revealed that Actinokineospora mzabensis is a heterotypic synonym of Actinokineospora spheciospongiae, Lentzea deserti is a heterotypic synonym of Lentzea atacamensis, Prauserella endophytica is a heterotypic synonym of Prauserella coralliicola, and Prauserella flava and Prauserella sediminis are heterotypic synonyms of Prauserella salsuginis. This study addresses the nomenclature conundrums of Actinoalloteichus cyanogriseus and Streptomyces caeruleus as well as Micropolyspora internatus and Saccharomonospora viridis.
Collapse
Affiliation(s)
- Wee Fei Aaron Teo
- Department of Microbiology, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala, Lumpur, Malaysia
| | - Geok Yuan Annie Tan
- Center for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala, Lumpur, Malaysia
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala, Lumpur, Malaysia
| | - Wen-Jun Li
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, PR China
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Science, Sun Yat-Sen University, Guangzhou, PR China
| |
Collapse
|
157
|
Karpov DS, Goncharenko AV, Usachev EV, Vasina DV, Divisenko EV, Chalenko YM, Pochtovyi AA, Ovchinnikov RS, Makarov VV, Yudin SM, Tkachuk AP, Gushchin VA. A Strategy for the Rapid Development of a Safe Vibrio cholerae Candidate Vaccine Strain. Int J Mol Sci 2021; 22:ijms222111657. [PMID: 34769085 PMCID: PMC8583953 DOI: 10.3390/ijms222111657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/01/2022] Open
Abstract
Approximately 1/6 of humanity is at high risk of experiencing cholera epidemics. The development of effective and safe vaccines against Vibrio cholerae, the primary cause of cholera, is part of the public health measures to prevent cholera epidemics. Natural nontoxigenic V. cholerae isolates represent a source of new genetically improved and relatively safe vaccine strains. However, the genomic engineering of wild-type V. cholerae strains is difficult, and these strains are genetically unstable due to their high homologous recombination activity. We comprehensively characterized two V. cholerae isolates using genome sequencing, bioinformatic analysis, and microscopic, physiological, and biochemical tests. Genetic constructs were Gibson assembled and electrotransformed into V. cholerae. Bacterial colonies were assessed using standard microbiological and immunological techniques. As a result, we created a synthetic chromoprotein-expressing reporter operon. This operon was used to improve the V. cholerae genome engineering approach and monitor the stability of the genetic constructs. Finally, we created a stable candidate V. cholerae vaccine strain bearing a recA deletion and expressing the β-subunit of cholera toxin. Thus, we developed a strategy for the rapid creation of genetically stable and relatively safe candidate vaccine strains. This strategy can be applied not only to V. cholerae but also to other important human bacterial pathogens.
Collapse
Affiliation(s)
- Dmitry S. Karpov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilov str., 32, 119991 Moscow, Russia
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- Correspondence: ; Tel.: +7-(499)-135-98-01
| | - Anna V. Goncharenko
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
| | - Evgenii V. Usachev
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Daria V. Vasina
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Elizaveta V. Divisenko
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Yaroslava M. Chalenko
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Andrei A. Pochtovyi
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Roman S. Ovchinnikov
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Valentin V. Makarov
- Centre for Strategic Planning of FMBA of Russia, 119121 Moscow, Russia; (V.V.M.); (S.M.Y.)
| | - Sergei M. Yudin
- Centre for Strategic Planning of FMBA of Russia, 119121 Moscow, Russia; (V.V.M.); (S.M.Y.)
| | - Artem P. Tkachuk
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
| | - Vladimir A. Gushchin
- Bach Institute of Biochemistry, Federal Research Centre “Fundamentals of Biotechnology” of the Russian Academy of Sciences, 119071 Moscow, Russia; (A.V.G.); (E.V.U.); (D.V.V.); (A.P.T.); (V.A.G.)
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Gamaleya str., 18, 123098 Moscow, Russia; (E.V.D.); (Y.M.C.); (A.A.P.); (R.S.O.)
- Department of Virology, Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia
| |
Collapse
|
158
|
Rubio-Portillo E, Martin-Cuadrado AB, Ramos-Esplá AÁ, Antón J. Metagenomics Unveils Posidonia oceanica "Banquettes" as a Potential Source of Novel Bioactive Compounds and Carbohydrate Active Enzymes (CAZymes). mSystems 2021; 6:e0086621. [PMID: 34519521 PMCID: PMC8547425 DOI: 10.1128/msystems.00866-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/25/2021] [Indexed: 11/20/2022] Open
Abstract
Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea. It produces large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." In recent years, interest in the potential uses of these P. oceanica banquettes has increased, and it was demonstrated that biomass extracts showed antioxidant, antifungal, and antiviral activities. The discovery of new compounds through the culture of microorganisms is limited, and to overcome this limitation, we performed a metagenomic study to investigate the microbial community associated with P. oceanica banquettes. Our results showed that the microbial community associated with P. oceanica banquettes was dominated by Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes, and Cyanobacteria. Pseudoalteromonas was the dominant genus, followed by Alteromonas, Labrenzia, and Aquimarina. The metagenome reads were binned and assembled into 23 nearly complete metagenome-assembled genomes (MAGs), which belonged to new families of Cyanobacteria, Myxococcota, and Granulosicoccaceae and also to the novel genus recently described as Gammaproteobacteria family UBA10353. A comparative analysis with 60 published metagenomes from different environments, including seawater, marine biofilms, soils, corals, sponges, and hydrothermal vents, indicated that banquettes have numbers of natural products and carbohydrate active enzymes (CAZymes) similar to those found for soils and were only surpassed by marine biofilms. New proteins assigned to cellulosome modules and lignocellulose-degrading enzymes were also found. These results unveiled the diverse microbial composition of P. oceanica banquettes and determined that banquettes are a potential source of bioactive compounds and novel enzymes. IMPORTANCE Posidonia oceanica is a long-living and very slow-growing marine seagrass endemic to the Mediterranean Sea that forms large amounts of leaf material and rhizomes, which can reach the shore and build important banks known as "banquettes." These banquettes accumulate on the shore, where they can prevent erosion, although they also cause social concern due to their impact on beach use. Furthermore, Posidonia dry material has been considered a source of traditional remedies in several areas of the Mediterranean, and a few studies have been carried out to explore pharmacological activities of Posidonia extracts. The work presented here provides the first characterization of the microbiome associated with Posidonia banquettes. We carried out a metagenomic analysis together with an in-depth comparison of the banquette metagenome with 60 published metagenomes from different environments. This comparative analysis has unveiled the potential that Posidonia banquettes have for the synthesis of natural products, both in abundance (only surpassed by marine biofilms) and novelty. These products include mainly nonribosomal peptides and carbohydrate active enzymes. Thus, the interest of our work lies in the interest of Posidonia "waste" material as a source of new bioactive compounds and CAZymes.
Collapse
Affiliation(s)
- Esther Rubio-Portillo
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| | | | - Alfonso Ángel Ramos-Esplá
- Department of Marine Sciences and Applied Biology, University of Alicante, Alicante, Spain
- CIMAR, University of Alicante, Alicante, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, Alicante, Spain
| |
Collapse
|
159
|
Maggiori C, Raymond-Bouchard I, Brennan L, Touchette D, Whyte L. MinION sequencing from sea ice cryoconites leads to de novo genome reconstruction from metagenomes. Sci Rep 2021; 11:21041. [PMID: 34702846 PMCID: PMC8548342 DOI: 10.1038/s41598-021-00026-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/30/2021] [Indexed: 01/04/2023] Open
Abstract
Genome reconstruction from metagenomes enables detailed study of individual community members, their metabolisms, and their survival strategies. Obtaining high quality metagenome-assembled genomes (MAGs) is particularly valuable in extreme environments like sea ice cryoconites, where the native consortia are recalcitrant to culture and strong astrobiology analogues. We evaluated three separate approaches for MAG generation from Allen Bay, Nunavut sea ice cryoconites-HiSeq-only, MinION-only, and hybrid (HiSeq + MinION)-where field MinION sequencing yielded a reliable metagenome. The hybrid assembly produced longer contigs, more coding sequences, and more total MAGs, revealing a microbial community dominated by Bacteroidetes. The hybrid MAGs also had the highest completeness, lowest contamination, and highest N50. A putatively novel species of Octadecabacter is among the hybrid MAGs produced, containing the genus's only known instances of genomic potential for nitrate reduction, denitrification, sulfate reduction, and fermentation. This study shows that the inclusion of MinION reads in traditional short read datasets leads to higher quality metagenomes and MAGs for more accurate descriptions of novel microorganisms in this extreme, transient habitat and has produced the first hybrid MAGs from an extreme environment.
Collapse
Affiliation(s)
- Catherine Maggiori
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
| | - Isabelle Raymond-Bouchard
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Laura Brennan
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - David Touchette
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| | - Lyle Whyte
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, 21 111 Lakeshore Road, Macdonald Stewart Building, Room MS3-053, Ste. Anne-de-Bellevue, Quebec, H9X 3V9, Canada
| |
Collapse
|
160
|
Lee GO, Eisenberg JNS, Uruchima J, Vasco G, Smith SM, Van Engen A, Victor C, Reynolds E, MacKay R, Jesser KJ, Castro N, Calvopiña M, Konstantinidis KT, Cevallos W, Trueba G, Levy K. Gut microbiome, enteric infections and child growth across a rural-urban gradient: protocol for the ECoMiD prospective cohort study. BMJ Open 2021; 11:e046241. [PMID: 34686548 PMCID: PMC8543627 DOI: 10.1136/bmjopen-2020-046241] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION The functional consequences of the bacterial gut microbiome for child health are not well understood. Characteristics of the early child gut microbiome may influence the course of enteric infections, and enteric infections may change the composition of the gut microbiome, all of which may have long-term implications for child growth and development. METHODS AND ANALYSIS We are conducting a community-based birth cohort study to examine interactions between gut microbiome conditions and enteric infections, and how environmental conditions affect the development of the gut microbiome. We will follow 360 newborns from 3 sites along a rural-urban gradient in northern coastal Ecuador, characterising enteric infections and gut microbial communities in the children every 3 to 6 months over their first 2 years of life. We will use longitudinal regression models to assess the correlation between environmental conditions and gut microbiome diversity and presence of specific taxa, controlling for factors that are known to be associated with the gut microbiome, such as diet. From 6 to 12 months of age, we will collect weekly stool samples to compare microbiome conditions in diarrhoea stools versus stools from healthy children prior to, during and after acute enteric infections, using principal-coordinate analysis and other multivariate statistical methods. ETHICS AND DISSEMINATION Ethics approvals have been obtained from Emory University and the Universidad San Francisco de Quito institutional review boards. The findings will be disseminated through conference presentations and peer-reviewed journals.
Collapse
Affiliation(s)
- Gwenyth O Lee
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Joseph N S Eisenberg
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jessica Uruchima
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Gabriela Vasco
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
- Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Shanon M Smith
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Amanda Van Engen
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Courtney Victor
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Elise Reynolds
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Rebecca MacKay
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, Georgia, USA
| | - Kelsey J Jesser
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, Washington, USA
| | - Nancy Castro
- Carrera de Nutrición y Dietética, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Manuel Calvopiña
- Carrera de Medicina, Universidad de Las Americas Facultad de Ciencias de la Salud, Quito, Pichincha, Ecuador
| | | | - William Cevallos
- Instituto de Biomedicina, Facultad de Ciencias Médicas, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Pichincha, Ecuador
| | - Karen Levy
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, Washington, USA
| |
Collapse
|
161
|
Yim KJ, Jung DH, Jang SW, Park S. Limnovirga soli gen. nov., sp. nov., isolated from river sediment. Int J Syst Evol Microbiol 2021; 71. [PMID: 34665108 DOI: 10.1099/ijsem.0.004891] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A cream-coloured, Gram-stain-negative, rod-shaped bacterium, designated strain KSC-6T, was isolated from soil sampled at the Gapcheon River watershed in Daejeon, Republic of Korea. The organism does not require NaCl for growth and grows at pH 6.0-8.0 (optimum, pH 7.0) and 10-37 °C (optimum, 25 °C). Phylogenetic trees based on the 16S rRNA gene sequences reveal that strain KSC-6T belongs to the family Chitinophagaceae within the order Chitinophagales and is most closely related to Panacibacter ginsenosidivorans Gsoil 1550T (95.9% similarity). The genomic DNA G+C content was 38.9 mol%. The major cellular fatty acids (>8 %) of strain KCS-6T were iso-C15:0, iso-C15 : 1 G and iso-C17 : 0 3-OH. The predominant respiratory quinone was menaquinone 7 and the predominant polar lipids were phosphatidylethanolamine, five unidentified aminolipids and two unidentified lipids. Based on genome analyses, low digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity values with closely related genera, and differential chemotaxonomic and physiological properties, we suggest that strain KCS-6T represents a novel species in a new genus in the family Chitinophagaceae, for which the name Limnovirga soli gen. nov., sp. nov. (type strain KCS-6T=KCCM 43337T=NBRC 114336T) is proposed.
Collapse
Affiliation(s)
- Kyung June Yim
- Bacteria Research Team. Freshwater Bacteria Research Department, Nakdonggang National Institute of Biological Resources (NNIBR), 137 Donam 2-gil, Sangju 37242, Republic of Korea
| | - Dong-Hyun Jung
- Bacteria Research Team. Freshwater Bacteria Research Department, Nakdonggang National Institute of Biological Resources (NNIBR), 137 Donam 2-gil, Sangju 37242, Republic of Korea
| | - Seok Won Jang
- Bacteria Research Team. Freshwater Bacteria Research Department, Nakdonggang National Institute of Biological Resources (NNIBR), 137 Donam 2-gil, Sangju 37242, Republic of Korea
| | - Sanghwa Park
- Bacteria Research Team. Freshwater Bacteria Research Department, Nakdonggang National Institute of Biological Resources (NNIBR), 137 Donam 2-gil, Sangju 37242, Republic of Korea
| |
Collapse
|
162
|
Alejandre-Colomo C, Francis B, Viver T, Harder J, Fuchs BM, Rossello-Mora R, Amann R. Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species. ISME COMMUNICATIONS 2021; 1:51. [PMID: 36747039 PMCID: PMC9723794 DOI: 10.1038/s43705-021-00052-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 02/08/2023]
Abstract
Winogradskyella is a genus within the phylum Bacteroidetes with a clear marine origin. Most members of this genus have been found associated with marine animals and algae, but also with inorganic surfaces such as sand. In this study, we analyzed genomes of eleven species recently isolated from surface seawater samples from the North Sea during a single spring algae bloom. Corresponding metagenomes yielded a single Candidatus species for this genus. All species in culture, with the exception of W. ursingii, affiliated with a Winogradskyella lineage characterized by large genomes (~4.3 ± 0.4 Mb), with high complexity in their carbohydrate and protein degradation genes. Specifically, the polysaccharide utilization loci (PULs) were diverse within each individual strain, indicating large substrate versatility. Although present in the North Sea, the abundances of these strains were at, or below, the detection limit of the metagenomes. In contrast, the single species, classified as Candidatus W. atlantica, to which all North Sea MAGs belonged, affiliated with a lineage in which the cultivated representatives showed small genomes of ~3.0-3.5 Mb, with the MAGs having ~2.3 Mb. In Ca. W. atlantica, genome streamlining has apparently resulted in the loss of biosynthesis pathways for several amino acids including arginine, methionine, leucine and valine, and the PUL loci were reduced to a single one for utilizing laminarin. This as-yet uncultivated species seems to capitalize on sporadically abundant substrates that are released by algae blooms, mainly laminarin. We also suggest that this streamlined genome might be responsible for the lack of growth on plates for this Candidatus species, in contrast to growth of the less abundant but coexisting members of the genus.
Collapse
Affiliation(s)
- Carlota Alejandre-Colomo
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ben Francis
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain
| | - Jens Harder
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Bernhard M Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA, UIB-CSIC), Miquel Marques 21, 07190, Esporles, Spain.
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359, Bremen, Germany.
| |
Collapse
|
163
|
Tang J, Li L, Li M, Du L, Shah MMR, Waleron MM, Waleron M, Waleron KF, Daroch M. Description, Taxonomy, and Comparative Genomics of a Novel species, Thermoleptolyngbya sichuanensis sp. nov., Isolated From Hot Springs of Ganzi, Sichuan, China. Front Microbiol 2021; 12:696102. [PMID: 34566907 PMCID: PMC8461337 DOI: 10.3389/fmicb.2021.696102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/03/2021] [Indexed: 12/23/2022] Open
Abstract
Thermoleptolyngbya is a newly proposed genus of thermophilic cyanobacteria that are often abundant in thermal environments. However, a vast majority of Thermoleptolyngbya strains were not systematically identified, and genomic features of this genus are also sparse. Here, polyphasic approaches were employed to identify a thermophilic strain, PKUAC-SCTA183 (A183 hereafter), isolated from hot spring Erdaoqiao, Ganzi prefecture, China. Whole-genome sequencing of the strain revealed its allocation to Thermoleptolyngbya sp. and genetic adaptations to the hot spring environment. While the results of 16S rRNA were deemed inconclusive, the more comprehensive polyphasic approach encompassing phenetic, chemotaxic, and genomic approaches strongly suggest that a new taxon, Thermoleptolyngbya sichuanensis sp. nov., should be delineated around the A183 strain. The genome-scale phylogeny and average nucleotide/amino-acid identity confirmed the genetic divergence of the A183 strain from other strains of Thermoleptolyngbya along with traditional methods such as 16S-23S ITS and its secondary structure analyses. Comparative genomic and phylogenomic analyses revealed inconsistent genome structures between Thermoleptolyngbya A183 and O-77 strains. Further gene ontology analysis showed that the unique genes of the two strains were distributed in a wide range of functional categories. In addition, analysis of genes related to thermotolerance, signal transduction, and carbon/nitrogen/sulfur assimilation revealed the ability of this strain to adapt to inhospitable niches in hot springs, and these findings were preliminarily confirmed using experimental, cultivation-based approaches.
Collapse
Affiliation(s)
- Jie Tang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Liheng Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Meijin Li
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Lianming Du
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Md Mahfuzur R Shah
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Michal M Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Malgorzata Waleron
- Department of Plant Protection and Biotechnology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof F Waleron
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Maurycy Daroch
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen, China
| |
Collapse
|
164
|
Ramírez-Fernández L, Orellana LH, Johnston ER, Konstantinidis KT, Orlando J. Diversity of microbial communities and genes involved in nitrous oxide emissions in Antarctic soils impacted by marine animals as revealed by metagenomics and 100 metagenome-assembled genomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 788:147693. [PMID: 34029816 DOI: 10.1016/j.scitotenv.2021.147693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/02/2021] [Accepted: 05/07/2021] [Indexed: 06/12/2023]
Abstract
Antarctic soils generally have low temperatures and limited availability of liquid water and nutrients. However, animals can increase the nutrient availability of ice-free areas by transferring nutrients from marine to terrestrial ecosystems, mainly through their excreta. In this study, we employed shotgun metagenomics and population genome binning techniques to study the diversity of microbial communities in Antarctic soils impacted by marine pinnipeds and birds relative to soils with no evident animal presence. We obtained ~285,000 16S rRNA gene-carrying metagenomic reads representing ~60 phyla and 100 metagenome-assembled genomes (MAGs) representing eight phyla. Only nine of these 100 MAGs represented previously described species, revealing that these soils harbor extensive novel diversity. Proteobacteria, Actinobacteria, and Bacteroidetes were the most abundant phyla in all samples, with Rhodanobacter being one of the most abundant genera in the bird-impacted soils. Further, the relative abundance of genes related to denitrification was at least double in soils impacted by birds than soils without animal influence. These results advance our understanding of the microbial populations and their genes involved in nitrous oxide emissions in ice-free coastal Antarctic soils impacted by marine animals and reveal novel microbial diversity associated with these ecosystems.
Collapse
Affiliation(s)
- Lia Ramírez-Fernández
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Luis H Orellana
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eric R Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Julieta Orlando
- Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.
| |
Collapse
|
165
|
Torrens C, Bellosillo B, Gibert J, Alier A, Santana F, Prim N, Corvec S. Are Cutibacterium acnes present at the end of primary shoulder prosthetic surgeries responsible for infection? Prospective study. Eur J Clin Microbiol Infect Dis 2021; 41:169-173. [PMID: 34535842 DOI: 10.1007/s10096-021-04348-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/07/2021] [Indexed: 11/24/2022]
Abstract
The purpose of this study was to investigate if the C. acnes present at the end of a primary shoulder arthroplasty could be responsible for shoulder arthroplasty infection. Prospective study includes patients undergoing primary shoulder arthroplasty from January 2015 until December 2018. From all the patients included, 5 to 12 tissue samples were obtained and were specifically cultured to detect the presence of C. acnes. DNA was extracted from the C acnes isolated colonies and Whole Genome Sequencing (WGS) analysis was done. A cohort of 156 patients was finally included. In twenty-seven patients, the C. acnes was present at the end of the primary surgery. Two of these patients developed a C. acnes periprosthetic shoulder infection at 6 and 4 months after the primary surgery. WGS of C. acnes isolated colonies showed that all the revision-surgery isolates clustered near to the corresponding primary-surgery isolates compared to the other independent bacterial colonies. (99.89% of similarity). C. acnes present at the end of the primary surgery can be the cause of early or delayed periprosthetic joint infections in shoulder arthroplasty.
Collapse
Affiliation(s)
- Carlos Torrens
- Orthopaedic Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain.
| | - Beatriz Bellosillo
- Pathology Department, Hospital del Mar, Barcelona, Spain.,Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Joan Gibert
- Pathology Department, Hospital del Mar, Barcelona, Spain.,Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Albert Alier
- Orthopaedic Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Fernando Santana
- Orthopaedic Department, Hospital del Mar, Passeig Marítim 25-29, 08003, Barcelona, Spain
| | - Nuria Prim
- Microbiology Service, Laboratori de Referència de Catalunya, Hospital del Mar, Barcelona, Spain
| | - Stéphane Corvec
- Service de Bactériologie Et Des Contrôles Microbiologiques, Université de Nantes, CHU Nantes, CRCINA U1232, 44000, Nantes, France
| |
Collapse
|
166
|
Draft Genome Sequence of Vibrio chagasii 18LP, Isolated from Gilthead Seabream (Sparus aurata) Larvae Reared in Aquaculture. Microbiol Resour Announc 2021; 10:e0065821. [PMID: 34528822 PMCID: PMC8444970 DOI: 10.1128/mra.00658-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
We report the draft genome sequence of Vibrio chagasii strain 18LP, isolated from gilthead seabream larvae at a fish hatchery research station in Portugal. The genome presents numerous features underlying opportunistic behavior, including genes coding for toxin biosynthesis and tolerance, host cell invasion, and heavy metal resistance.
Collapse
|
167
|
Kayani MUR, Huang W, Feng R, Chen L. Genome-resolved metagenomics using environmental and clinical samples. Brief Bioinform 2021; 22:bbab030. [PMID: 33758906 PMCID: PMC8425419 DOI: 10.1093/bib/bbab030] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/29/2020] [Accepted: 01/20/2021] [Indexed: 12/25/2022] Open
Abstract
Recent advances in high-throughput sequencing technologies and computational methods have added a new dimension to metagenomic data analysis i.e. genome-resolved metagenomics. In general terms, it refers to the recovery of draft or high-quality microbial genomes and their taxonomic classification and functional annotation. In recent years, several studies have utilized the genome-resolved metagenome analysis approach and identified previously unknown microbial species from human and environmental metagenomes. In this review, we describe genome-resolved metagenome analysis as a series of four necessary steps: (i) preprocessing of the sequencing reads, (ii) de novo metagenome assembly, (iii) genome binning and (iv) taxonomic and functional analysis of the recovered genomes. For each of these four steps, we discuss the most commonly used tools and the currently available pipelines to guide the scientific community in the recovery and subsequent analyses of genomes from any metagenome sample. Furthermore, we also discuss the tools required for validation of assembly quality as well as for improving quality of the recovered genomes. We also highlight the currently available pipelines that can be used to automate the whole analysis without having advanced bioinformatics knowledge. Finally, we will highlight the most widely adapted and actively maintained tools and pipelines that can be helpful to the scientific community in decision making before they commence the analysis.
Collapse
Affiliation(s)
- Masood ur Rehman Kayani
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Wanqiu Huang
- Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 200,000, China
| | - Ru Feng
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| | - Lei Chen
- Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Institute of Immunology, Shanghai Jiao Tong University, School of Medicine, Shanghai 2,000,025, China
| |
Collapse
|
168
|
The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos. Microbiol Resour Announc 2021; 10:e0032021. [PMID: 34435855 PMCID: PMC8388533 DOI: 10.1128/mra.00320-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba) strains that were obtained from the octocoral Eunicella labiata. Genome annotation revealed multiple symbiosis factors common to all genomes, such as eukaryotic-like repeat protein- and multidrug resistance-encoding genes, which likely underpin symbiotic relationships with marine invertebrate hosts.
Collapse
|
169
|
Gibson L, Crombie AT, McNamara NP, Murrell JC. Isoprene-degrading bacteria associated with the phyllosphere of Salix fragilis, a high isoprene-emitting willow of the Northern Hemisphere. ENVIRONMENTAL MICROBIOME 2021; 16:17. [PMID: 34446108 PMCID: PMC8394569 DOI: 10.1186/s40793-021-00386-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/12/2021] [Indexed: 05/13/2023]
Abstract
BACKGROUND Isoprene accounts for about half of total biogenic volatile organic compound emissions globally, and as a climate active gas it plays a significant and varied role in atmospheric chemistry. Terrestrial plants are the largest source of isoprene, with willow (Salix) making up one of the most active groups of isoprene producing trees. Bacteria act as a biological sink for isoprene and those bacteria associated with high isoprene-emitting trees may provide further insight into its biodegradation. RESULTS A DNA-SIP experiment incubating willow (Salix fragilis) leaves with 13C-labelled isoprene revealed an abundance of Comamonadaceae, Methylobacterium, Mycobacterium and Polaromonas in the isoprene degrading community when analysed by 16S rRNA gene amplicon sequencing. Metagenomic analysis of 13C-enriched samples confirmed the abundance of Comamonadaceae, Acidovorax, Polaromonas, Variovorax and Ramlibacter. Mycobacterium and Methylobacterium were also identified after metagenomic analysis and a Mycobacterium metagenome-assembled genome (MAG) was recovered. This contained two complete isoprene degradation metabolic gene clusters, along with a propane monooxygenase gene cluster. Analysis of the abundance of the alpha subunit of the isoprene monooxygenase, isoA, in unenriched DNA samples revealed that isoprene degraders associated with willow leaves are abundant, making up nearly 0.2% of the natural bacterial community. CONCLUSIONS Analysis of the isoprene degrading community associated with willow leaves using DNA-SIP and focused metagenomics techniques enabled recovery of the genome of an active isoprene-degrading Mycobacterium species and provided valuable insight into bacteria involved in degradation of isoprene on the leaves of a key species of isoprene-emitting tree in the northern hemisphere.
Collapse
Affiliation(s)
- Lisa Gibson
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Andrew T Crombie
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Niall P McNamara
- Centre of Ecology and Hydrology, Lancaster University, Bailrigg, Lancaster, LA1 4AP, UK
| | - J Colin Murrell
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| |
Collapse
|
170
|
Hu S, Wang Y, Wang J, Liu K, Tang X, Gao J. Streptomyces xanthii sp. nov. and Streptomyces roseirectus sp. nov. isolated from a Chinese medicinal plant. Int J Syst Evol Microbiol 2021; 71. [PMID: 34410901 DOI: 10.1099/ijsem.0.004962] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two strains of Actinobacteria, designated CRXT-Y-14T and CRXT-G-22T, were isolated from the healthy leaves and seeds, respectively, of a medicinal plant Xanthium sibiricum. Their taxonomic positions were determined using a polyphasic approach. Strain CRXT-Y-14T produced flexuous chains of smooth-surfaced spores. Strain CRXT-G-22T produced straight chains of smooth-surfaced spores. Their morphological features were consistent with the diagnostic characteristics of members of the genus Streptomyces. The results of 16S rRNA gene sequence analyses indicated two strains represented members of the genus Streptomyces. CRXT-Y-14T shared 99.3, 98.9, 98.8 % sequence similarities to Streptomyces atriruber NRRL B-24165T, Streptomyces avermitilis MA-4680T and Streptomyces davaonensis JCM 4913T, respectively. Whilst CRXT-G-22T exhibited highest similarity to Streptomyces acidiscabies ATCC 49003T (98.9 %). The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the closest phylogenetic neighbours of strains CRXT-Y-14T and CRXT-G-22T were S. atriruber NRRL B-24165T and S. acidiscabies ATCC 49003T, respectively. The phylogenomic analyses further confirmed the relative relationship between strain CRXT-G-22T and S. acidiscabies ATCC 49003T, but indicated that CRXT-Y-14T could represent a novel species of the genus Streptomyce. However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between CRXT-Y-14T and strain CRXT-G-22T, between CRXT-Y-14T and S. atriruber NRRL B-24165T, and between CRXT-G-22T and S. acidiscabies ATCC 49003T were 85.4 and 23.2 %, 85.8 and 23.9 % and 89.1 and 34.1 %, respectively, far below the 95~96 and 70 % cut-off points recommended for delineating species. Furthermore, these two novel isolates were distinctly differentiated from their relatives in the genus Streptomyces with respect to phenotypic and chemotaxonomic characteristics. On the basis of these data, CRXT-Y-14T and CRXT-G-22T clearly represent two novel species within the genus Streptomyces, for which the names Streptomyces xanthii sp. nov. (type strain CRXT-Y-14T = MCCC 1K04966T= JCM 34527T) and Streptomyces roseirectus sp. nov. (type CRXT-G-22T = MCCC 1K04979T= JCM 34565T) are proposed.
Collapse
Affiliation(s)
- Siren Hu
- School of Life Science, Hunan University of Science and technology, Xiangtan 411201, PR China
| | - Yinfeng Wang
- School of Life Science, Hunan University of Science and technology, Xiangtan 411201, PR China
| | - Junzhen Wang
- Xichang Institute of Agricultural Science, Liangshan 615000, PR China
| | - Keyun Liu
- School of Life Science, Hunan University of Science and technology, Xiangtan 411201, PR China
| | - Xinke Tang
- School of Life Science, Hunan University of Science and technology, Xiangtan 411201, PR China
| | - Jian Gao
- School of Life Science, Hunan University of Science and technology, Xiangtan 411201, PR China.,Key Laboratory of Ecological Remediation and Safe Utilization of Heavy Metal-Polluted Soils, College of Hunan Province, Xiangtan 411201, PR China
| |
Collapse
|
171
|
Osuna-Mascaró C, Doña J, Johnson KP, de Rojas M. Genome-Resolved Metagenomic Analyses Reveal the Presence of a Putative Bacterial Endosymbiont in an Avian Nasal Mite (Rhinonyssidae; Mesostigmata). Microorganisms 2021; 9:microorganisms9081734. [PMID: 34442816 PMCID: PMC8398770 DOI: 10.3390/microorganisms9081734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/09/2021] [Accepted: 08/10/2021] [Indexed: 11/16/2022] Open
Abstract
Rhinonyssidae (Mesostigmata) is a family of nasal mites only found in birds. All species are hematophagous endoparasites, which may damage the nasal cavities of birds, and also could be potential reservoirs or vectors of other infections. However, the role of members of Rhinonyssidae as disease vectors in wild bird populations remains uninvestigated, with studies of the microbiomes of Rhinonyssidae being almost non-existent. In the nasal mite (Tinaminyssus melloi) from rock doves (Columba livia), a previous study found evidence of a highly abundant putatively endosymbiotic bacteria from Class Alphaproteobacteria. Here, we expanded the sample size of this species (two different hosts- ten nasal mites from two independent samples per host), incorporated contamination controls, and increased sequencing depth in shotgun sequencing and genome-resolved metagenomic analyses. Our goal was to increase the information regarding this mite species and its putative endosymbiont. We obtained a metagenome assembled genome (MAG) that was estimated to be 98.1% complete and containing only 0.9% possible contamination. Moreover, the MAG has characteristics typical of endosymbionts (namely, small genome size an AT bias). Overall, our results support the presence of a potential endosymbiont, which is the first described for avian nasal mites to date, and improve the overall understanding of the microbiota inhabiting these mites.
Collapse
Affiliation(s)
- Carolina Osuna-Mascaró
- Department of Biology, University of Nevada, 1664 N Virginia St, Reno, NV 89557, USA
- Correspondence: (C.O.-M.); (M.d.R.)
| | - Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA; (J.D.); (K.P.J.)
- Departamento de Biología Animal, Universitario de Cartuja, Calle Prof. Vicente Callao, 3, 18011 Granada, Spain
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL 61820, USA; (J.D.); (K.P.J.)
| | - Manuel de Rojas
- Department of Microbiology and Parasitology, Faculty of Pharmacy, Universidad de Sevilla, Calle San Fernando, 4, 41004 Sevilla, Spain
- Correspondence: (C.O.-M.); (M.d.R.)
| |
Collapse
|
172
|
Genome-centric investigation of anaerobic digestion using sustainable second and third generation substrates. J Biotechnol 2021; 339:53-64. [PMID: 34371053 DOI: 10.1016/j.jbiotec.2021.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/23/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
Biogas production through co-digestion of second and third generation substrates is an environmentally sustainable approach. Green willow biomass, chicken manure waste and microalgae biomass substrates were combined in the anaerobic digestion experiments. Biochemical methane potential test showed that biogas yields of co-digestions were significantly higher compared to the yield when energy willow was the sole substrate. To scale up the experiment continuous stirred-tank reactors (CSRTs) are employed, digestion parameters are monitored. Furthermore, genome-centric metagenomics approach was employed to gain functional insight into the complex anaerobic decomposing process. This revealed the importance of Firmicutes, Actinobacteria, Proteobacteria and Bacteroidetes phyla as major bacterial participants, while Methanomicrobia and Methanobacteria represented the archaeal constituents of the communities. The bacterial phyla were shown to perform the carbohydrate hydrolysis. Among the representatives of long-chain carbohydrate hydrolysing microbes Bin_61: Clostridia is newly identified metagenome assembled genome (MAG) and Bin_13: DTU010 sp900018335 is common and abundant in all CSTRs. Methanogenesis was linked to the slow-growing members of the community, where hydrogenotrophic methanogen species Methanoculleus (Bin_10) and Methanobacterium (Bin_4) predominate. A sensitive balance between H2 producers and consumers was shown to be critical for stable biomethane production and efficient waste biodegradation.
Collapse
|
173
|
Tóth Á, Bata-Vidács I, Kosztik J, Máté R, Kutasi J, Tóth E, Bóka K, Táncsics A, Nagy I, Kovács G, Kukolya J. Sphingobacterium pedocola sp. nov. a novel halotolerant bacterium isolated from agricultural soil. Antonie van Leeuwenhoek 2021; 114:1575-1584. [PMID: 34363180 PMCID: PMC8448689 DOI: 10.1007/s10482-021-01623-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/17/2021] [Indexed: 11/29/2022]
Abstract
A Gram-reaction-negative halotolerant bacterial strain, designated Ka21T, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, highest similarity was found with Sphingobacterium alkalisoli Y3L14T (96.72%). Cells were observed to be aerobic, non-motile rods. The isolate was found to be able to grow between 0 and 10% of NaCl concentration. The assembled genome of strain Ka21T has a total length of 5.2 Mb with a G + C content of 41.0 mol%. According to the genome analysis, Ka21T encodes several glycoside hydrolases that may play a role in the degradation of accumulated plant biomass in the soil. Based on phenotypic characteristics and phylogenetic analysis, it is concluded that strain Ka21T represents a novel species in the Sphingobacterium genus for which the name Sphingobacterium pedocola sp. nov. is proposed. The type strain of the species is strain Ka21T (= LMG 31575T = NCAIM B.02636T).
Collapse
Affiliation(s)
- Ákos Tóth
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary.
| | - Ildikó Bata-Vidács
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Judit Kosztik
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Rózsa Máté
- BioFil Microbiological, Biotechnological and Biochemical Ltd, Budapest, Hungary
| | - József Kutasi
- BioFil Microbiological, Biotechnological and Biochemical Ltd, Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - Károly Bóka
- Department of Plant Anatomy, Eötvös Loránd University, Budapest, Hungary
| | - András Táncsics
- Regional University Center of Excellence in Environmental Industry, Szent István University, Gödöllő, Hungary
| | - István Nagy
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,Institute of Biochemistry, Biological Research Centre, Eötvös Lorand Research Network, Szeged, Hungary
| | - Gábor Kovács
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary.,University of Sopron, Sopron, Hungary
| | - József Kukolya
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| |
Collapse
|
174
|
Whole-genome characterization and comparative genomics of a novel freshwater cyanobacteria species: Pseudanabaena punensis. Mol Phylogenet Evol 2021; 164:107272. [PMID: 34332035 DOI: 10.1016/j.ympev.2021.107272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 11/23/2022]
Abstract
Cyanobacteria are emerging as a potential source of novel, beneficial bioactive compounds. However, some cyanobacteria species can harm water quality and public health through the production of toxins. Therefore, surveying the occurrence and generating genomic resources of cyanobacteria producing harmful compounds could help develop the control methods necessary to manage their growth and limit the release contaminants into the water bodies. Here, we describe a novel strain, Pseudanabaena punensis isolated from the open ends of pipelines supplying freshwater. This isolate was characterized morphologically, biochemically and by whole-genome sequence analysis. We also provide genomic information for P. punensis to help understand and highlight the features unique to this isolate. Morphological and genetic (analysis using 16S rRNA and rbcL genes) data were used to assign this novel strain to phylogenetic and taxonomic groups. The isolate was identified as a filamentous and non-heterocystous cyanobacteria. Based on morphological and 16S rRNA phylogeny, this isolate shares characteristics with the Pseudanabaenaceae family, but remains distinct from well-characterized species suggesting its polyphyletic assemblage. The whole-genome sequence analysis suggests greater genomic and phenotypic plasticity. Genome-wide sequence and comparative genomic analyses, comparing against several closely related species, revealed diverse and important genes associated with synthesizing bioactive compounds, multi-drug resistance pathway, heavy metal resistance, and virulence factors. This isolate also produces several important fatty acids with potential industrial applications. The observations described in this study emphasize both industrial applications and risks associated with the freshwater contamination, and therefore genomic resources provided in this study offer an opportunity for further investigations.
Collapse
|
175
|
Abstract
DPANN is known as highly diverse, globally widespread, and mostly ectosymbiotic archaeal superphylum. However, this group of archaea was overlooked for a long time, and there were limited in-depth studies reported. In this investigation, 41 metagenome-assembled genomes (MAGs) belonging to the DPANN superphylum were recovered (18 MAGs had average nucleotide identity [ANI] values of <95% and a percentage of conserved proteins [POCP] of >50%, while 14 MAGs showed a POCP of <50%), which were analyzed comparatively with 515 other published DPANN genomes. Mismatches to known 16S rRNA gene primers were identified among 16S rRNA genes of DPANN archaea. Numbers of gene families lost (mostly related to energy and amino acid metabolism) were over three times greater than those gained in the evolution of DPANN archaea. Lateral gene transfer (LGT; ∼45.5% was cross-domain) had facilitated niche adaption of the DPANN archaea, ensuring a delicate equilibrium of streamlined genomes with efficient niche-adaptive strategies. For instance, LGT-derived cytochrome bd ubiquinol oxidase and arginine deiminase in the genomes of “Candidatus Micrarchaeota” could help them better adapt to aerobic acidic mine drainage habitats. In addition, most DPANN archaea acquired enzymes for biosynthesis of extracellular polymeric substances (EPS) and transketolase/transaldolase for the pentose phosphate pathway from Bacteria. IMPORTANCE The domain Archaea is a key research model for gaining insights into the origin and evolution of life, as well as the relevant biogeochemical processes. The discovery of nanosized DPANN archaea has overthrown many aspects of microbiology. However, the DPANN superphylum still contains a vast genetic novelty and diversity that need to be explored. Comprehensively comparative genomic analysis on the DPANN superphylum was performed in this study, with an attempt to illuminate its metabolic potential, ecological distribution and evolutionary history. Many interphylum differences within the DPANN superphylum were found. For example, Altiarchaeota had the biggest genome among DPANN phyla, possessing many pathways missing in other phyla, such as formaldehyde assimilation and the Wood-Ljungdahl pathway. In addition, LGT acted as an important force to provide DPANN archaeal genetic flexibility that permitted the occupation of diverse niches. This study has advanced our understanding of the diversity and genome evolution of archaea.
Collapse
|
176
|
Identification of Plant Growth Promoting Rhizobacteria That Improve the Performance of Greenhouse-Grown Petunias under Low Fertility Conditions. PLANTS 2021; 10:plants10071410. [PMID: 34371613 PMCID: PMC8309264 DOI: 10.3390/plants10071410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 11/22/2022]
Abstract
The production of greenhouse ornamentals relies on high fertilizer inputs to meet scheduling deadlines and quality standards, but overfertilization has negative environmental impacts. The goals of this study were to identify plant-growth-promoting rhizobacteria (PGPR) that can improve greenhouse ornamental crop performance with reduced fertilizer inputs, and to identify the best measurements of plant performance for assessing the beneficial impact of PGPR on ornamentals. A high-throughput greenhouse trial was used to identify 14 PGPR isolates that improved the flower/bud number and shoot dry weight of Petunia × hybrida ‘Picobella Blue’ grown under low fertility conditions in peat-based media. These 14 PGPR were then applied to petunias grown under low fertility conditions (25 mg L−1 N). PGPR-treated plants were compared to negative (untreated at 25 mg L−1 N) and positive (untreated at 50, 75, 100, and 150 mg L−1 N) controls. Multiple parameters were measured in the categories of flowering, vegetative growth, and vegetative quality to determine the best measurements to assess improvements in ornamental plant performance. Caballeronia zhejiangensis C7B12-treated plants performed better in almost all parameters and were comparable to untreated plants fertilized with 50 mg L−1 N. Genomic analysis identified genes that were potentially involved in plant growth promotion. Our study identified potential PGPR that can be used as biostimulants to produce high-quality greenhouse ornamentals with lower fertilizer inputs.
Collapse
|
177
|
Ramos-Barbero MD, Viver T, Zabaleta A, Senel E, Gomariz M, Antigüedad I, Santos F, Martínez-García M, Rosselló-Móra R, Antón J. Ancient saltern metagenomics: tracking changes in microbes and their viruses from the underground to the surface. Environ Microbiol 2021; 23:3477-3498. [PMID: 34110059 DOI: 10.1111/1462-2920.15630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/26/2021] [Accepted: 06/06/2021] [Indexed: 11/28/2022]
Abstract
Microbial communities in hypersaline underground waters derive from ancient organisms trapped within the evaporitic salt crystals and are part of the poorly known subterranean biosphere. Here, we characterized the viral and prokaryotic assemblages present in the hypersaline springs that dissolve Triassic-Keuper evaporite rocks and feed the Añana Salt Valley (Araba/Alava, Basque Country, Spain). Four underground water samples (around 23% total salinity) with different levels of exposure to the open air were analysed by means of microscopy and metagenomics. Cells and viruses in the spring water had lower concentrations than what are normally found in hypersaline environments and seemed to be mostly inactive. Upon exposure to the open air, there was an increase in activity of both cells and viruses as well as a selection of phylotypes. The underground water was inhabited by a rich community harbouring a diverse set of genes coding for retinal binding proteins. A total of 35 viral contigs from 15 to 104 kb, representing partial or total viral genomes, were assembled and their evolutionary changes through the spring system were followed by SNP analysis and metagenomic island tracking. Overall, both the viral and the prokaryotic assemblages changed quickly upon exposure to the open air conditions.
Collapse
Affiliation(s)
- Mª Dolores Ramos-Barbero
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Ane Zabaleta
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Ece Senel
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain.,Department of Biology, Institute of Graduate Programs, Eskisehir Technical University, Yunusemre Campus, Eskisehir, 26470, Turkey
| | - María Gomariz
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Iñaki Antigüedad
- Hydro-Environmental Processes Group, Geology Department, Science and Technology Faculty, University of the Basque Country UPV/EHU, Leioa, 48940, Spain
| | - Fernando Santos
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Manuel Martínez-García
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| | - Ramon Rosselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Diversity, Mediterranean Institute of Advanced Studies (IMEDEA; CSIC-UIB), Esporles, Illes Balears, 07190, Spain
| | - Josefa Antón
- Department of Physiology, Genetics and Microbiology, University of Alicante, 03690 San Vicent del Raspeig, Alicante, Spain
| |
Collapse
|
178
|
Counts JA, Willard DJ, Kelly RM. Life in hot acid: a genome-based reassessment of the archaeal order Sulfolobales. Environ Microbiol 2021; 23:3568-3584. [PMID: 32776389 PMCID: PMC10560490 DOI: 10.1111/1462-2920.15189] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/31/2020] [Accepted: 08/06/2020] [Indexed: 01/07/2023]
Abstract
The order Sulfolobales was one of the first named Archaeal lineages, with globally distributed members from terrestrial thermal acid springs (pH < 4; T > 65°C). The Sulfolobales represent broad metabolic capabilities, ranging from lithotrophy, based on inorganic iron and sulfur biotransformations, to autotrophy, to chemoheterotrophy in less acidophilic species. Components of the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation cycle, as well as sulfur oxidation, are nearly universally conserved, although dissimilatory sulfur reduction and disproportionation (Acidianus, Stygiolobus and Sulfurisphaera) and iron oxidation (Acidianus, Metallosphaera, Sulfurisphaera, Sulfuracidifex and Sulfodiicoccus) are limited to fewer lineages. Lithotrophic marker genes appear more often in highly acidophilic lineages. Despite the presence of facultative anaerobes and one confirmed obligate anaerobe, oxidase complexes (fox, sox, dox and a new putative cytochrome bd) are prevalent in many species (even facultative/obligate anaerobes), suggesting a key role for oxygen among the Sulfolobales. The presence of fox genes tracks with a putative antioxidant OsmC family peroxiredoxin, an indicator of oxidative stress derived from mixing reactive metals and oxygen. Extreme acidophily appears to track inversely with heterotrophy but directly with lithotrophy. Recent phylogenetic re-organization efforts are supported by the comparative genomics here, although several changes are proposed, including the expansion of the genus Saccharolobus.
Collapse
Affiliation(s)
- James A. Counts
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 USA
| |
Collapse
|
179
|
Amarouchi Z, Esmaeel Q, Sanchez L, Jacquard C, Hafidi M, Vaillant-Gaveau N, Ait Barka E. Beneficial Microorganisms to Control the Gray Mold of Grapevine: From Screening to Mechanisms. Microorganisms 2021; 9:microorganisms9071386. [PMID: 34202293 PMCID: PMC8304954 DOI: 10.3390/microorganisms9071386] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 11/16/2022] Open
Abstract
In many vineyards around the world, Botrytis cinerea (B. cinerea) causes one of the most serious diseases of aerial grapevine (Vitis vinifera L.) organs. The control of the disease relies mainly on the use of chemical products whose use is increasingly challenged. To develop new sustainable methods to better resist B. cinerea, beneficial bacteria were isolated from vineyard soil. Once screened based on their antimicrobial effect through an in vivo test, two bacterial strains, S3 and S6, were able to restrict the development of the pathogen and significantly reduced the Botrytis-related necrosis. The photosynthesis analysis showed that the antagonistic strains also prevent grapevines from considerable irreversible PSII photo-inhibition four days after infection with B. cinerea. The 16S rRNA gene sequences of S3 exhibited 100% similarity to Bacillus velezensis, whereas S6 had 98.5% similarity to Enterobacter cloacae. On the other hand, the in silico analysis of the whole genome of isolated strains has revealed the presence of “biocontrol-related” genes supporting their plant growth and biocontrol activities. The study concludes that those bacteria could be potentially useful as a suitable biocontrol agent in harvested grapevine.
Collapse
Affiliation(s)
- Zakaria Amarouchi
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
- Laboratoire de Biotechnologie Végétale et Valorisation des Bio-Ressources, Faculté des Sciences, Université Moulay Ismail, Meknès B.P. 11201, Morocco;
| | - Qassim Esmaeel
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Lisa Sanchez
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Cédric Jacquard
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Majida Hafidi
- Laboratoire de Biotechnologie Végétale et Valorisation des Bio-Ressources, Faculté des Sciences, Université Moulay Ismail, Meknès B.P. 11201, Morocco;
| | - Nathalie Vaillant-Gaveau
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
| | - Essaid Ait Barka
- Université de Reims Champagne-Ardenne, RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Z.A.); (Q.E.); (L.S.); (C.J.); (N.V.-G.)
- Correspondence: ; Tel.: +33-326913221
| |
Collapse
|
180
|
Paulson JN, Williams BL, Hehnly C, Mishra N, Sinnar SA, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge DSS, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell LM, Burgoine K, Couto-Rodriguez M, Ericson JE, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs AM, Kaaya BN, Kangere SM, Kulkarni AV, Kumbakumba E, Li X, Limbrick DD, Magombe J, Morton SU, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson MR, Roy F, Sheldon K, Townsend R, Weeks AD, Whalen AJ, Quackenbush J, Ssenyonga P, Galperin MY, Almeida M, Atkins H, Warf BC, Lipkin WI, Broach JR, Schiff SJ. Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Sci Transl Med 2021; 12:12/563/eaba0565. [PMID: 32998967 DOI: 10.1126/scitranslmed.aba0565] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2020] [Indexed: 12/14/2022]
Abstract
Postinfectious hydrocephalus (PIH), which often follows neonatal sepsis, is the most common cause of pediatric hydrocephalus worldwide, yet the microbial pathogens underlying this disease remain to be elucidated. Characterization of the microbial agents causing PIH would enable a shift from surgical palliation of cerebrospinal fluid (CSF) accumulation to prevention of the disease. Here, we examined blood and CSF samples collected from 100 consecutive infant cases of PIH and control cases comprising infants with non-postinfectious hydrocephalus in Uganda. Genomic sequencing of samples was undertaken to test for bacterial, fungal, and parasitic DNA; DNA and RNA sequencing was used to identify viruses; and bacterial culture recovery was used to identify potential causative organisms. We found that infection with the bacterium Paenibacillus, together with frequent cytomegalovirus (CMV) coinfection, was associated with PIH in our infant cohort. Assembly of the genome of a facultative anaerobic bacterial isolate recovered from cultures of CSF samples from PIH cases identified a strain of Paenibacillus thiaminolyticus This strain, designated Mbale, was lethal when injected into mice in contrast to the benign reference Paenibacillus strain. These findings show that an unbiased pan-microbial approach enabled characterization of Paenibacillus in CSF samples from PIH cases, and point toward a pathway of more optimal treatment and prevention for PIH and other proximate neonatal infections.
Collapse
Affiliation(s)
- Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Christine Hehnly
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Shamim A Sinnar
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Lijun Zhang
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Paddy Ssentongo
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | | | - Dona S S Wijetunge
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Benjamin von Bredow
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ronnie Mulondo
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Julius Kiwanuka
- Department of Pediatrics, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Francis Bajunirwe
- Department of Epidemiology, Mbarara University of Science and Technology, P.O. Box 1410, Mbarara, Uganda
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Lisa M Bebell
- Division of Infectious Disease, Massachusetts Genereal Hospital, Harvard Medical School, 55 Fruit St, GRJ-504, Boston, MA 02114, USA
| | - Kathy Burgoine
- Neonatal Unit, Department of Paediatrics and Child Health, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966, Mbale, Uganda.,Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966 Mbale, Uganda.,University of Liverpool, Liverpool, L69 3BX, UK
| | - Mara Couto-Rodriguez
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Biotia, 100 6th avenue, New York, NY 10013, USA
| | - Jessica E Ericson
- Division of Pediatric Infectious Disease, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Tim Erickson
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Matthew Ferrari
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Melissa Gladstone
- Institute for Translational Medicine, University of Liverpool, Liverpool, L12 2AP, UK
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Murali Haran
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Mady Hornig
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Albert M Isaacs
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Brian Nsubuga Kaaya
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Sheila M Kangere
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Abhaya V Kulkarni
- Division of Neurosurgery, Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
| | - Elias Kumbakumba
- Department of Pediatrics, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Xiaoxiao Li
- Institute for Translational Medicine, University of Liverpool, Liverpool, L12 2AP, UK
| | - David D Limbrick
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Joshua Magombe
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston MA 02115, USA
| | - John Mugamba
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Peter Olupot-Olupot
- Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966 Mbale, Uganda.,Busitema University, Mbale Campus, Plot 29-33 Pallisa Road, P.O. Box 1966, Mbale, Uganda
| | - Justin Onen
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Mallory R Peterson
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA
| | - Farrah Roy
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kathryn Sheldon
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Reid Townsend
- Department of Medicine, Washington University School of Medicine , St. Louis, MO 63130, USA
| | - Andrew D Weeks
- Sanyu Research Unit, Liverpool Women's Hospital, University of Liverpool, Liverpool L8 7SS, UK
| | - Andrew J Whalen
- Department of Mechanical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter Ssenyonga
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mathieu Almeida
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, 78350, France
| | - Hannah Atkins
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - James R Broach
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Steven J Schiff
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA. .,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA.,Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
| |
Collapse
|
181
|
Ghosh S, Sarangi AN, Mukherjee M, Singh D, Madhavi M, Tripathy S. Reconstructing Draft Genomes Using Genome Resolved Metagenomics Reveal Arsenic Metabolizing Genes and Secondary Metabolites in Fresh Water Lake in Eastern India. Bioinform Biol Insights 2021; 15:11779322211025332. [PMID: 34220198 PMCID: PMC8221699 DOI: 10.1177/11779322211025332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
Rabindra Sarovar lake is an artificial freshwater lake in the arsenic infested eastern region of India. In this study, using the genome resolved metagenomics approach; we have deciphered the taxonomic diversity as well as the functional insights of the gene pools specific to this region. Initially, a total of 113 Metagenome Assembled Genomes (MAGs) were recovered from the two predominant seasons, that is, rainy (n = 50) and winter (n = 63). After bin refinement and de-replication, 27 MAGs (18 from Winter season and 9 from Rainy season) were reconstructed. These MAGs were either of high-quality (n = 10) or of medium quality (n = 17) that was determined based on genome completeness and contamination. These 27 MAGs spanning across 6 bacterial phyla and the most predominant ones were Proteobacteria, Bacteroidetes, and Cyanobacteria regardless of the season. Functional annotation across the MAGs suggested the existence of all known types of arsenic resistance and metabolism genes. Besides, important secondary metabolites such as zoocin_A, prochlorosin, and microcin were also abundantly present in these genomes. The metagenomic study of this lake provides the first insights into the microbiome composition and functional classification of the gene pools in two predominant seasons. The presence of arsenic metabolism and resistance genes in the recovered genomes is a sign of adaptation of the microbes to the arsenic contamination in this region. The presence of secondary metabolite genes in the lake microbiome has several implications including the potential use of these for the pharmaceutical industry.
Collapse
Affiliation(s)
- Samrat Ghosh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Aditya Narayan Sarangi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Mayuri Mukherjee
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Deeksha Singh
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Madduluri Madhavi
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India
| | - Sucheta Tripathy
- Computational Genomics Lab, Structural Biology and Bioinformatics Division, CSIR Indian Institute of Chemical Biology, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| |
Collapse
|
182
|
Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces. Proc Natl Acad Sci U S A 2021; 118:2024464118. [PMID: 34161269 DOI: 10.1073/pnas.2024464118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
While it is well recognized that the environmental resistome is global, diverse, and augmented by human activities, it has been difficult to assess risk because of the inability to culture many environmental organisms, and it is difficult to evaluate risk from current sequence-based environmental methods. The four most important criteria to determine risk are whether the antibiotic-resistance genes (ARGs) are a complete, potentially functional complement; if they are linked with other resistances; whether they are mobile; and the identity of their host. Long-read sequencing fills this important gap between culture and short sequence-based methods. To address these criteria, we collected feces from a ceftiofur-treated cow, enriched the samples in the presence of antibiotics to favor ARG functionality, and sequenced long reads using Nanopore and PacBio technologies. Multidrug-resistance genes comprised 58% of resistome abundance, but only 0.8% of them were plasmid associated; fluroquinolone-, aminoglycoside-, macrolide-lincosamide-streptogramin (MLS)-, and β-lactam-resistance genes accounted for 2.7 to 12.3% of resistome abundance but with 19 to 78% located on plasmids. A variety of plasmid types were assembled, some of which share low similarity to plasmids in current databases. Enterobacteriaceae were dominant hosts of antibiotic-resistant plasmids; physical linkage of extended-spectrum β-lactamase genes (CTX-M, TEM, CMY, and CARB) was largely found with aminoglycoside-, MLS-, tetracycline-, trimethoprim-, phenicol-, sulfonamide-, and mercury-resistance genes. A draft circular chromosome of Vagococcus lutrae was assembled; it carries MLS-, tetracycline- (including tetM and tetL on an integrative conjugative element), and trimethoprim-resistance genes flanked by many transposase genes and insertion sequences, implying that they remain transferrable.
Collapse
|
183
|
Sheinman M, Arkhipova K, Arndt PF, Dutilh BE, Hermsen R, Massip F. Identical sequences found in distant genomes reveal frequent horizontal transfer across the bacterial domain. eLife 2021; 10:62719. [PMID: 34121661 PMCID: PMC8270642 DOI: 10.7554/elife.62719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 06/13/2021] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer (HGT) is an essential force in microbial evolution. Despite detailed studies on a variety of systems, a global picture of HGT in the microbial world is still missing. Here, we exploit that HGT creates long identical DNA sequences in the genomes of distant species, which can be found efficiently using alignment-free methods. Our pairwise analysis of 93,481 bacterial genomes identified 138,273 HGT events. We developed a model to explain their statistical properties as well as estimate the transfer rate between pairs of taxa. This reveals that long-distance HGT is frequent: our results indicate that HGT between species from different phyla has occurred in at least 8% of the species. Finally, our results confirm that the function of sequences strongly impacts their transfer rate, which varies by more than three orders of magnitude between different functional categories. Overall, we provide a comprehensive view of HGT, illuminating a fundamental process driving bacterial evolution.
Collapse
Affiliation(s)
- Michael Sheinman
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands.,Division of Molecular Carcinogenesis, the Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Ksenia Arkhipova
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Peter F Arndt
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Rutger Hermsen
- Theoretical Biology and Bioinformatics, Biology Department, Utrecht University, Utrecht, Netherlands
| | - Florian Massip
- Berlin Institute for Medical Systems Biology, Max Delbrück Center, Berlin, Germany.,Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, Villleurbanne, France
| |
Collapse
|
184
|
Tláskal V, Pylro VS, Žifčáková L, Baldrian P. Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood. Front Microbiol 2021; 12:668644. [PMID: 34177846 PMCID: PMC8226273 DOI: 10.3389/fmicb.2021.668644] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/17/2021] [Indexed: 11/19/2022] Open
Abstract
The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.
Collapse
Affiliation(s)
- Vojtěch Tláskal
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Victor Satler Pylro
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
- Microbial Ecology and Bioinformatics Laboratory, Department of Biology, Federal University of Lavras (UFLA), Lavras, Brazil
| | - Lucia Žifčáková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Praha, Czechia
| |
Collapse
|
185
|
Peta V, Raths R, Bücking H. Massilia horti sp. nov. and Noviherbaspirillum arenae sp. nov., two novel soil bacteria of the Oxalobacteraceae. Int J Syst Evol Microbiol 2021; 71. [PMID: 33956597 DOI: 10.1099/ijsem.0.004765] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We isolated two new soil bacteria: ONC3T (from garden soil in NC, USA; LMG 31738T=NRRL B-65553T) and M1T (from farmed soil in MI, USA; NRRL B-65551T=ATCC TSD-197T=LMG 31739T) and characterized their metabolic phenotype based on Biolog, MALDI-TOF MS and fatty acid analyses, and compared 16S rRNA and whole genome sequences to other members of the Oxalobacteraceae after sequencing on an Illumina Nextera platform. Based on the results of 16S rRNA sequence analysis, ONC3T shows the highest sequence similarity to Massilia solisilvae J18T (97.8 %), Massilia terrae J11T (97.7 %) and Massilia agilis J9T (97.3 %). Strain M1T is most closely related to Noviherbaspirillum denitrificans TSA40T, Noviherbaspirillum agri K-1-15T and Noviherbaspirillum autotrophicum TSA66T (sequence identity of 98.2, 98.0 and 97.8 %, respectively). The whole genome of ONC3T has an assembled size of 5.62 Mbp, a G+C content of 63.8 mol% and contains 5104 protein-coding sequences, 56 tRNA genes and two rRNA operons. The genome of M1T has a length of 4.71 MBp, a G+C content of 63.81 mol% and includes 4967 protein-coding genes, two rRNA operons and 44 tRNA genes. Whole genome comparisons identified Massilia sp. WG5 with a 79.3 % average nucleotide identity (ANI) and 22.6 % digital DNA-DNA hybridization (dDDH), and Massilia sp. UBA11196 with 78.2 % average amino acid identity (AAI) as the most closely related species to ONC3T. M1T is most closely related to N. autotrophicum TSA66T with an ANI of 80.27 %, or N. denitrificans TSA40T with a dDDH of 22.3 %. The application of community-accepted standards such as <98.7 % in 16S sequence similarity and <95-96 % ANI or 70 % DDH support the classification of Massilia horti ONC3T and Noviherbaspirillum arenae M1T as novel species within the Oxalobacteraceae.
Collapse
Affiliation(s)
- Vincent Peta
- South Dakota State University, Biology and Microbiology Department, Brookings SD 57007, USA
| | - Rachel Raths
- South Dakota State University, Biology and Microbiology Department, Brookings SD 57007, USA
| | - Heike Bücking
- University of Missouri, Division of Plant Sciences, College of Agriculture, Food and Natural Resources, Columbia, MO 65211, USA.,South Dakota State University, Biology and Microbiology Department, Brookings SD 57007, USA
| |
Collapse
|
186
|
Shang Z, Ferris ZE, Sweeney D, Chase AB, Yuan C, Hui Y, Hou L, Older EA, Xue D, Tang X, Zhang W, Nagarkatti P, Nagarkatti M, Testerman TL, Jensen PR, Li J. Grincamycins P-T: Rearranged Angucyclines from the Marine Sediment-Derived Streptomyces sp. CNZ-748 Inhibit Cell Lines of the Rare Cancer Pseudomyxoma Peritonei. JOURNAL OF NATURAL PRODUCTS 2021; 84:1638-1648. [PMID: 33899471 PMCID: PMC8650148 DOI: 10.1021/acs.jnatprod.1c00179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
While marine natural products have been investigated for anticancer drug discovery, they are barely screened against rare cancers. Thus, in our effort to discover potential drug leads against the rare cancer pseudomyxoma peritonei (PMP), which currently lacks effective drug treatments, we screened extracts of marine actinomycete bacteria against the PMP cell line ABX023-1. This effort led to the isolation of nine rearranged angucyclines from Streptomyces sp. CNZ-748, including five new analogues, namely, grincamycins P-T (1-5). The chemical structures of these compounds were unambiguously established based on spectroscopic and chemical analyses. Particularly, grincamycin R (3) possesses an S-containing α-l-methylthio-aculose residue, which was discovered in nature for the first time. All of the isolated compounds were evaluated against four PMP cell lines and some exhibited low micromolar inhibitory activities. To identify a candidate biosynthetic gene cluster (BGC) encoding the grincamycins, we sequenced the genome of the producing strain, Streptomyces sp. CNZ-748, and compared the BGCs detected with those linked to the production of angucyclines with different aglycon structures.
Collapse
Affiliation(s)
- Zhuo Shang
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Zachary E Ferris
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Douglas Sweeney
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Alexander B Chase
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Chunhua Yuan
- Nuclear Magnetic Resonance Facility, Campus Chemical Instrument Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Yvonne Hui
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Lukuan Hou
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Ethan A Older
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Dan Xue
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
| | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Mitzi Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Traci L Testerman
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, South Carolina 29209, United States
| | - Paul R Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Jie Li
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| |
Collapse
|
187
|
Metagenomes, Metatranscriptomes, and Metagenome-Assembled Genomes from Chesapeake and Delaware Bay (USA) Water Samples. Microbiol Resour Announc 2021; 10:e0026221. [PMID: 34042480 PMCID: PMC8201625 DOI: 10.1128/mra.00262-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we present 36 metagenomes, 59 metatranscriptomes, and 373 metagenome-assembled genomes (MAGs) from Chesapeake and Delaware Bay water samples. This data set will be useful for studying microbial biogeochemical cycling in estuaries.
Collapse
|
188
|
Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling. Appl Environ Microbiol 2021; 87:e0054621. [PMID: 33837013 DOI: 10.1128/aem.00546-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N2O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N2O reductases (nosZ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase (norB) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N2O emissions. Nitrogen fixation (nifH) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO2 and the largest natural source of N2O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems.
Collapse
|
189
|
Tóth Á, Máté R, Kutasi J, Bata-Vidács I, Tóth E, Táncsics A, Kovács G, Nagy I, Kukolya J. Cellvibrio polysaccharolyticus sp. nov., a cellulolytic bacterium isolated from agricultural soil. Int J Syst Evol Microbiol 2021; 71. [PMID: 33999790 DOI: 10.1099/ijsem.0.004805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel Gram-reaction-negative bacterial strain, designated Ka43T, was isolated from agricultural soil and characterised using a polyphasic approach to determine its taxonomic position. On the basis of 16S rRNA gene sequence analysis, the strain shows highest similarity (97.1 %) to Cellvibrio diazotrophicus E50T. Cells of strain Ka43T are aerobic, motile, short rods. The major fatty acids are summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH), C18 : 1 ω7c and C16 : 0. The only isoprenoid quinone is Q-8. The polar lipid profile includes phosphatidylethanolamine, phosphatidylglycerol, four phospholipids, two lipids and an aminolipid. The assembled genome of strain Ka43T has a total length of 4.2 Mb and the DNA G+C content is 51.6 mol%. Based on phenotypic data, including chemotaxonomic characteristics and analysis of the 16S rRNA gene sequences, it was concluded that strain Ka43T represents a novel species in the genus Cellvibrio, for which the name Cellvibrio polysaccharolyticus sp. nov. is proposed. The type strain of the species is strain Ka43T (=LMG 31577T=NCAIM B.02637T).
Collapse
Affiliation(s)
- Ákos Tóth
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Rózsa Máté
- BioFil Microbiological, Biotechnological and Biochemical Ltd, Budapest, Hungary
| | - József Kutasi
- BioFil Microbiological, Biotechnological and Biochemical Ltd, Budapest, Hungary
| | - Ildikó Bata-Vidács
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| | - Erika Tóth
- Department of Microbiology, Eötvös Loránd University, Budapest, Hungary
| | - András Táncsics
- Department of Molecular Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Gábor Kovács
- University of Sopron, Sopron, Hungary.,SeqOmics Biotechnology Ltd, Szeged, Hungary
| | - István Nagy
- Institute of Biochemistry, Biological Research Centre, Eötvös Loránd Research Network, Szeged, Hungary.,SeqOmics Biotechnology Ltd, Szeged, Hungary
| | - József Kukolya
- Research Group for Food Biotechnology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Budapest, Hungary
| |
Collapse
|
190
|
Ludwig W, Viver T, Westram R, Francisco Gago J, Bustos-Caparros E, Knittel K, Amann R, Rossello-Mora R. Release LTP_12_2020, featuring a new ARB alignment and improved 16S rRNA tree for prokaryotic type strains. Syst Appl Microbiol 2021; 44:126218. [PMID: 34111737 DOI: 10.1016/j.syapm.2021.126218] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/27/2021] [Accepted: 05/14/2021] [Indexed: 01/29/2023]
Abstract
The new release of the All-Species Living Tree Project (LTP) represents an important step forward in the reconstruction of 16S rRNA gene phylogenies, since we not only provide an updated set of type strain sequences until December 2020, but also a series of improvements that increase the quality of the database. An improved universal alignment has been introduced that is implemented in the ARB format. In addition, all low-quality sequences present in the previous releases have been substituted by new entries with higher quality, many of them as a result of whole genome sequencing. Altogether, the improvements in the dataset and 16S rRNA sequence alignment allowed us to reconstruct robust phylogenies. The trees made available through this current LTP release feature the best topologies currently achievable. The given nomenclature and taxonomic hierarchy reflect all the changes available up to December 2020. The aim is to regularly update the validly published nomenclatural classification changes and new taxa proposals. The new release can be found at the following URL: https://imedea.uib-csic.es/mmg/ltp/.
Collapse
Affiliation(s)
- Wolfgang Ludwig
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Tomeu Viver
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Ralf Westram
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany; Ribocon GmbH, Fahrenheitstraße. 1, D-28359 Bremen, Germany
| | - Juan Francisco Gago
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Esteban Bustos-Caparros
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D-28359 Bremen, Germany
| | - Ramon Rossello-Mora
- Marine Microbiology Group, Department of Animal and Microbial Diversity, IMEDEA (CSIC-UIB), C/Miquel Marqués 21, 07190 Esporles, Spain.
| |
Collapse
|
191
|
Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, Clavel T. Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria. ISME COMMUNICATIONS 2021; 1:16. [PMID: 36732617 PMCID: PMC9723785 DOI: 10.1038/s43705-021-00017-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/21/2021] [Accepted: 05/04/2021] [Indexed: 02/05/2023]
Abstract
The study of microbial communities is hampered by the large fraction of still unknown bacteria. However, many of these species have been isolated, yet lack a validly published name or description. The validation of names for novel bacteria requires that the uniqueness of those taxa is demonstrated and their properties are described. The accepted format for this is the protologue, which can be time-consuming to create. Hence, many research fields in microbiology and biotechnology will greatly benefit from new approaches that reduce the workload and harmonise the generation of protologues.We have developed Protologger, a bioinformatic tool that automatically generates all the necessary readouts for writing a detailed protologue. By producing multiple taxonomic outputs, functional features and ecological analysis using the 16S rRNA gene and genome sequences from a single species, the time needed to gather the information for describing novel taxa is substantially reduced. The usefulness of Protologger was demonstrated by using three published isolate collections to describe 34 novel taxa, encompassing 17 novel species and 17 novel genera, including the automatic generation of ecologically and functionally relevant names. We also highlight the need to utilise multiple taxonomic delineation methods, as while inconsistencies between each method occur, a combined approach provides robust placement. Protologger is open source; all scripts and datasets are available, along with a webserver at www.protologger.de.
Collapse
Affiliation(s)
- Thomas C A Hitch
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, Jerusalem, Israel
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany
- Braunschweig University of Technology, Braunschweig, Germany
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Thomas Clavel
- Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.
| |
Collapse
|
192
|
Nordstedt NP, Jones ML. Genomic Analysis of Serratia plymuthica MBSA-MJ1: A Plant Growth Promoting Rhizobacteria That Improves Water Stress Tolerance in Greenhouse Ornamentals. Front Microbiol 2021; 12:653556. [PMID: 34046022 PMCID: PMC8144289 DOI: 10.3389/fmicb.2021.653556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
Water stress decreases the health and quality of horticulture crops by inhibiting photosynthesis, transpiration, and nutrient uptake. Application of plant growth promoting rhizobacteria (PGPR) can increase the growth, stress tolerance, and overall quality of field and greenhouse grown crops subjected to water stress. Here, we evaluated Serratia plymuthica MBSA-MJ1 for its ability to increase plant growth and quality of Petunia × hybrida (petunia), Impatiens walleriana (impatiens), and Viola × wittrockiana (pansy) plants recovering from severe water stress. Plants were treated weekly with inoculum of MBSA-MJ1, and plant growth and quality were evaluated 2 weeks after recovery from water stress. Application of S. plymuthica MBSA-MJ1 increased the visual quality and shoot biomass of petunia and impatiens and increased the flower number of petunia after recovery from water stress. In addition, in vitro characterizations showed that MBSA-MJ1 is a motile bacterium with moderate levels of antibiotic resistance that can withstand osmotic stress. Further, comprehensive genomic analyses identified genes putatively involved in bacterial osmotic and oxidative stress responses and the synthesis of osmoprotectants and vitamins that could potentially be involved in increasing plant water stress tolerance. This work provides a better understanding of potential mechanisms involved in beneficial plant-microbe interactions under abiotic stress using a novel S. plymuthica strain as a model.
Collapse
Affiliation(s)
- Nathan P Nordstedt
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Michelle L Jones
- Department of Horticulture and Crop Science, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| |
Collapse
|
193
|
Bunse C, Koch H, Breider S, Simon M, Wietz M. Sweet spheres: succession and CAZyme expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Environ Microbiol 2021; 23:3130-3148. [PMID: 33876546 DOI: 10.1111/1462-2920.15536] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/06/2021] [Accepted: 04/15/2021] [Indexed: 12/24/2022]
Abstract
Polysaccharide particles are important substrates and microhabitats for marine bacteria. However, substrate-specific bacterial dynamics in mixtures of particle types with different polysaccharide composition, as likely occurring in natural habitats, are undescribed. Here, we studied the composition, functional diversity and gene expression of marine bacterial communities colonizing a mix of alginate and pectin particles. Amplicon, metagenome and metatranscriptome sequencing revealed that communities on alginate and pectin particles significantly differed from their free-living counterparts. Unexpectedly, microbial dynamics on alginate and pectin particles were similar, with predominance of amplicon sequence variants (ASVs) from Tenacibaculum, Colwellia, Psychrobium and Psychromonas. Corresponding metagenome-assembled genomes (MAGs) expressed diverse alginate lyases, several colocalized in polysaccharide utilization loci. Only a single, low-abundant MAG showed elevated transcript abundances of pectin-degrading enzymes. One specific Glaciecola ASV dominated the free-living fraction, possibly persisting on particle-derived oligomers through different glycoside hydrolases. Elevated ammonium uptake and metabolism signified nitrogen as an important factor for degrading carbon-rich particles, whereas elevated methylcitrate and glyoxylate cycles suggested nutrient limitation in surrounding waters. The bacterial preference for alginate, whereas pectin primarily served as colonization scaffold, illuminates substrate-driven dynamics within mixed polysaccharide pools. These insights expand our understanding of bacterial niche specialization and the biological carbon pump in macroalgae-rich habitats.
Collapse
Affiliation(s)
- Carina Bunse
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Hanna Koch
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany.,Department of Microbiology, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sven Breider
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Meinhard Simon
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Matthias Wietz
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| |
Collapse
|
194
|
Doña J, Virrueta Herrera S, Nyman T, Kunnasranta M, Johnson KP. Patterns of Microbiome Variation Among Infrapopulations of Permanent Bloodsucking Parasites. Front Microbiol 2021; 12:642543. [PMID: 33935998 PMCID: PMC8085356 DOI: 10.3389/fmicb.2021.642543] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/26/2021] [Indexed: 12/22/2022] Open
Abstract
While interspecific variation in microbiome composition can often be readily explained by factors such as host species identity, there is still limited knowledge of how microbiomes vary at scales lower than the species level (e.g., between individuals or populations). Here, we evaluated variation in microbiome composition of individual parasites among infrapopulations (i.e., populations of parasites of the same species living on a single host individual). To address this question, we used genome-resolved and shotgun metagenomic data of 17 infrapopulations (balanced design) of the permanent, bloodsucking seal louse Echinophthirius horridus sampled from individual Saimaa ringed seals Pusa hispida saimensis. Both genome-resolved and read-based metagenomic classification approaches consistently show that parasite infrapopulation identity is a significant factor that explains both qualitative and quantitative patterns of microbiome variation at the intraspecific level. This study contributes to the general understanding of the factors driving patterns of intraspecific variation in microbiome composition, especially of bloodsucking parasites, and has implications for understanding how well-known processes occurring at higher taxonomic levels, such as phylosymbiosis, might arise in these systems.
Collapse
Affiliation(s)
- Jorge Doña
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States.,Departamento de Biología Animal, Universidad de Granada, Granada, Spain
| | - Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, IL, United States
| |
Collapse
|
195
|
Madeira CL, Menezes O, Park D, Jog KV, Hatt JK, Gavazza S, Krzmarzick MJ, Sierra-Alvarez R, Spain JC, Konstantinidis KT, Field JA. Bacteria Make a Living Breathing the Nitroheterocyclic Insensitive Munitions Compound 3-Nitro-1,2,4-triazol-5-one (NTO). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:5806-5814. [PMID: 33835790 DOI: 10.1021/acs.est.0c07161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The nitroheterocyclic 3-nitro-1,2,4-triazol-5-one (NTO) is an ingredient of insensitive explosives increasingly used by the military, becoming an emergent environmental pollutant. Cometabolic biotransformation of NTO occurs in mixed microbial cultures in soils and sludges with excess electron-donating substrates. Herein, we present the unusual energy-yielding metabolic process of NTO respiration, in which the NTO reduction to 3-amino-1,2,4-triazol-5-one (ATO) is linked to the anoxic acetate oxidation to CO2 by a culture enriched from municipal anaerobic digester sludge. Cell growth was observed simultaneously with NTO reduction, whereas the culture was unable to grow in the presence of acetate only. Extremely low concentrations (0.06 mg L-1) of the uncoupler carbonyl cyanide m-chlorophenyl hydrazone inhibited NTO reduction, indicating that the process was linked to respiration. The ultimate evidence of NTO respiration was adenosine triphosphate production due to simultaneous exposure to NTO and acetate. Metagenome sequencing revealed that the main microorganisms (and relative abundances) were Geobacter anodireducens (89.3%) and Thauera sp. (5.5%). This study is the first description of a nitroheterocyclic compound being reduced by anaerobic respiration, shedding light on creative microbial processes that enable bacteria to make a living reducing NTO.
Collapse
Affiliation(s)
- Camila L Madeira
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Osmar Menezes
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Doyoung Park
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Kalyani V Jog
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Janet K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Savia Gavazza
- Laboratório de Saneamento Ambiental, Departamento de Engenharia Civil e Ambiental, Universidade Federal de Pernambuco, Recife, Pernambuco 50740-530, Brazil
| | - Mark J Krzmarzick
- School of Civil and Environmental Engineering, Oklahoma State University, Stillwater, Oklahoma 74078, United States
| | - Reyes Sierra-Alvarez
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| | - Jim C Spain
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
- Center for Environmental Diagnostics & Bioremediation, University of West Florida, Pensacola, Florida 32514, United States
| | - Konstantinos T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0355, United States
| | - Jim A Field
- Department of Chemical and Environmental Engineering, University of Arizona, Tucson, Arizona 85721-0011, United States
| |
Collapse
|
196
|
McLean JS, Bor B, Kerns KA, Liu Q, To TT, Solden L, Hendrickson EL, Wrighton K, Shi W, He X. Acquisition and Adaptation of Ultra-small Parasitic Reduced Genome Bacteria to Mammalian Hosts. Cell Rep 2021; 32:107939. [PMID: 32698001 PMCID: PMC7427843 DOI: 10.1016/j.celrep.2020.107939] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 06/20/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
The first cultivated representative of the enigmatic phylum Saccharibacteria (formerly TM7) was isolated from humans and revealed an ultra-small cell size (200-300 nm), a reduced genome with limited biosynthetic capabilities, and a unique parasitic lifestyle. TM7x was the only cultivated member of the candidate phyla radiation (CPR), estimated to encompass 26% of the domain Bacteria. Here we report on divergent genomes from major lineages across the Saccharibacteria phylum in humans and mammals, as well as from ancient dental calculus. These lineages are present at high prevalence within hosts. Direct imaging reveals that all groups are ultra-small in size, likely feeding off commensal bacteria. Analyses suggest that multiple acquisition events in the past led to the current wide diversity, with convergent evolution of key functions allowing Saccharibacteria from the environment to adapt to mammals. Ultra-small, parasitic CPR bacteria represent a relatively unexplored paradigm of prokaryotic interactions within mammalian microbiomes.
Collapse
Affiliation(s)
- Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA; Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| | - Kristopher A Kerns
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Quanhui Liu
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Thao T To
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Lindsey Solden
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Erik L Hendrickson
- Department of Periodontics, University of Washington, Seattle, WA 98195, USA
| | - Kelly Wrighton
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142, USA; Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115, USA
| |
Collapse
|
197
|
Bédard E, Trigui H, Liang J, Doberva M, Paranjape K, Lalancette C, Allegra S, Faucher SP, Prévost M. Local Adaptation of Legionella pneumophila within a Hospital Hot Water System Increases Tolerance to Copper. Appl Environ Microbiol 2021; 87:e00242-21. [PMID: 33674435 PMCID: PMC8117758 DOI: 10.1128/aem.00242-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/25/2021] [Indexed: 11/20/2022] Open
Abstract
In large-building water systems, Legionella pneumophila is exposed to common environmental stressors such as copper. The aim of this study was to evaluate the susceptibility to copper of L. pneumophila isolates recovered from various sites: two clinical and seven environmental isolates from hot water system biofilm and water and from cooling tower water. After a 1-week acclimation in simulated drinking water, strains were exposed to various copper concentrations (0.8 to 5 mg/liter) for over 672 h. Complete loss of culturability was observed for three isolates following copper exposure to 5 mg/liter for 672 h. Two sequence type 1427 (ST1427)-like isolates were highly sensitive to copper, while the other two, isolated from biofilm samples, maintained higher culturability. The expression of the copper resistance gene copA evaluated by reverse transcription-quantitative PCR (RT-qPCR) was significantly higher for the biofilm isolates. All four ST1427-like isolates were recovered from the same water system during an outbreak. Whole-genome sequencing results confirmed that the four isolates are very close phylogenetically, differing by only 29 single nucleotide polymorphisms, suggesting in situ adaptation to microenvironmental conditions, possibly due to epigenetic regulation. These results indicate that the immediate environment within a building water distribution system influences the tolerance of L. pneumophila to copper. Increased contact of L. pneumophila biofilm strains with copper piping or copper alloys in the heat exchanger might lead to local adaptation. The phenotypic differences observed between water and biofilm isolates from the hot water system of a health care facility warrants further investigation to assess the relevance of evaluating disinfection performances based on water sampling alone.IMPORTANCELegionella pneumophila is a pathogen indigenous to natural and large building water systems in the bulk and the biofilm phases. The immediate environment within a system can impact the tolerance of L. pneumophila to environmental stressors, including copper. In health care facilities, copper levels in water can vary, depending on water quality, plumbing materials, and age. This study evaluated the impact of the isolation site (water versus biofilm, hot water system versus cooling tower) within building water systems. Closely related strains isolated from a health care facility hot water system exhibited variable tolerance to copper stress, shown by differential expression of copA, with biofilm isolates displaying highest expression and tolerance. Relying on the detection of L. pneumophila in water samples following exposure to environmental stressors such as copper may underestimate the prevalence of L. pneumophila, leading to inappropriate risk management strategies and increasing the risk of exposure for vulnerable patients.
Collapse
Affiliation(s)
- Emilie Bédard
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Hana Trigui
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
| | - Jeffrey Liang
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Margot Doberva
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
| | - Kiran Paranjape
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Cindy Lalancette
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Séverine Allegra
- University of Lyon, UJM-Saint-Etienne, UMR 5600 CNRS, EVS-ISTHME, Saint-Etienne, France
| | - Sebastien P Faucher
- Department of Natural Resource Sciences, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, Quebec, Canada
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, Quebec, Canada
| |
Collapse
|
198
|
Thaler DS. Is Global Microbial Biodiversity Increasing, Decreasing, or Staying the Same? Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.565649] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Animal and plant biodiversity is decreasing. In contrast, the global direction and the pace of change in microbial, including viral, biodiversity is unknown. Important niches for microbial diversity occur in highly specific associations with plants and animals, and these niches are lost as hosts become extinct. The taxonomic diversity of human gut bacteria is reported to be decreasing. On the other hand, SARS-CoV-2 variation is increasing. Where microbes are concerned, Darwin’s “tangled bank” of interdependent organisms may be composed mostly of other microbes. There is the likelihood that as some classes of microbes become extinct, others evolve and diversify. A better handle on all processes that affect microbial biodiversity and their net balance is needed. Lack of insight into the dynamics of evolution of microbial biodiversity is arguably the single most profound and consequential unknown with regard to human knowledge of the biosphere. If some or all parts of microbial diversity are relentlessly increasing, then survey approaches may be too slow to ever catch up. New approaches, including single-molecule or single-cell sequencing in populations, as well as focused attention on modulators and vectors of vertical and horizontal evolution may offer more direct insights into some aspects of the pace of microbial evolution.
Collapse
|
199
|
Soto-Girón MJ, Peña-Gonzalez A, Hatt JK, Montero L, Páez M, Ortega E, Smith S, Cevallos W, Trueba G, Konstantinidis KT, Levy K. Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador. Am J Trop Med Hyg 2021; 104:2275-2285. [PMID: 33872206 DOI: 10.4269/ajtmh.20-0831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 02/15/2021] [Indexed: 12/12/2022] Open
Abstract
Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch's t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.
Collapse
Affiliation(s)
- Maria J Soto-Girón
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Angela Peña-Gonzalez
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia
| | - Janet K Hatt
- 2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Lorena Montero
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Maritza Páez
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Estefania Ortega
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shanon Smith
- 4School of Public Health, University of Washington, Seattle, Washington
| | - William Cevallos
- 5Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador
| | - Gabriel Trueba
- 3Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Konstantinos T Konstantinidis
- 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia.,2School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Karen Levy
- 4School of Public Health, University of Washington, Seattle, Washington
| |
Collapse
|
200
|
Tian L, Mazloom R, Heath LS, Vinatzer BA. LINflow: a computational pipeline that combines an alignment-free with an alignment-based method to accelerate generation of similarity matrices for prokaryotic genomes. PeerJ 2021; 9:e10906. [PMID: 33828908 PMCID: PMC8000461 DOI: 10.7717/peerj.10906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 01/14/2021] [Indexed: 01/21/2023] Open
Abstract
Background Computing genomic similarity between strains is a prerequisite for genome-based prokaryotic classification and identification. Genomic similarity was first computed as Average Nucleotide Identity (ANI) values based on the alignment of genomic fragments. Since this is computationally expensive, faster and computationally cheaper alignment-free methods have been developed to estimate ANI. However, these methods do not reach the level of accuracy of alignment-based methods. Methods Here we introduce LINflow, a computational pipeline that infers pairwise genomic similarity in a set of genomes. LINflow takes advantage of the speed of the alignment-free sourmash tool to identify the genome in a dataset that is most similar to a query genome and the precision of the alignment-based pyani software to precisely compute ANI between the query genome and the most similar genome identified by sourmash. This is repeated for each new genome that is added to a dataset. The sequentially computed ANI values are stored as Life Identification Numbers (LINs), which are then used to infer all other pairwise ANI values in the set. We tested LINflow on four sets, 484 genomes in total, and compared the needed time and the generated similarity matrices with other tools. Results LINflow is up to 150 times faster than pyani and pairwise ANI values generated by LINflow are highly correlated with those computed by pyani. However, because LINflow infers most pairwise ANI values instead of computing them directly, ANI values occasionally depart from the ANI values computed by pyani. In conclusion, LINflow is a fast and memory-efficient pipeline to infer similarity among a large set of prokaryotic genomes. Its ability to quickly add new genome sequences to an already computed similarity matrix makes LINflow particularly useful for projects when new genome sequences need to be regularly added to an existing dataset.
Collapse
Affiliation(s)
- Long Tian
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Reza Mazloom
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Lenwood S Heath
- Department of Computer Science, Virginia Tech, Blacksburg, VA, USA
| | - Boris A Vinatzer
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, USA
| |
Collapse
|