1
|
Kloub L, Gosselin S, Graf J, Gogarten JP, Bansal MS. Investigating Additive and Replacing Horizontal Gene Transfers Using Phylogenies and Whole Genomes. Genome Biol Evol 2024; 16:evae180. [PMID: 39163267 PMCID: PMC11375855 DOI: 10.1093/gbe/evae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 07/29/2024] [Accepted: 08/12/2024] [Indexed: 08/22/2024] Open
Abstract
Horizontal gene transfer (HGT) is fundamental to microbial evolution and adaptation. When a gene is horizontally transferred, it may either add itself as a new gene to the recipient genome (possibly displacing nonhomologous genes) or replace an existing homologous gene. Currently, studies do not usually distinguish between "additive" and "replacing" HGTs, and their relative frequencies, integration mechanisms, and specific roles in microbial evolution are poorly understood. In this work, we develop a novel computational framework for large-scale classification of HGTs as either additive or replacing. Our framework leverages recently developed phylogenetic approaches for HGT detection and classifies HGTs inferred between terminal edges based on gene orderings along genomes and phylogenetic relationships between the microbial species under consideration. The resulting method, called DART, is highly customizable and scalable and can classify a large fraction of inferred HGTs with high confidence and statistical support. Our application of DART to a large dataset of thousands of gene families from 103 Aeromonas genomes provides insights into the relative frequencies, functional biases, and integration mechanisms of additive and replacing HGTs. Among other results, we find that (i) the relative frequency of additive HGT increases with increasing phylogenetic distance, (ii) replacing HGT dominates at shorter phylogenetic distances, (iii) additive and replacing HGTs have strikingly different functional profiles, (iv) homologous recombination in flanking regions of a novel gene may be a frequent integration mechanism for additive HGT, and (v) phages and mobile genetic elements likely play an important role in facilitating additive HGT.
Collapse
Affiliation(s)
- Lina Kloub
- School of Computing, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269-4155, USA
| | - Sophia Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT 06269-3125, USA
| | - Joerg Graf
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT 06269-3125, USA
- Pacific Biosciences Research Center, University of Hawaii, Honolulu, HI 96822, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, 91 North Eagleville Road, Unit 3125, Storrs, CT 06269-3125, USA
- The Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| | - Mukul S Bansal
- School of Computing, University of Connecticut, 371 Fairfield Way, Unit 4155, Storrs, CT 06269-4155, USA
- The Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
| |
Collapse
|
2
|
Chen Y, Li X, Zhou D, Wei Y, Feng J, Cai B, Qi D, Zhang M, Zhao Y, Li K, Pan Z, Wang W, Xie J. Streptomyces-Secreted Fluvirucin B6 as a Potential Bio-Fungicide for Managing Banana Fusarium Wilt and Mycotoxins and Modulating the Soil Microbial Community Structure. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:17890-17902. [PMID: 39083645 DOI: 10.1021/acs.jafc.4c04077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Banana Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc TR4) is the most destructive soil-borne fungal disease. Until now, there has been a lack of effective measures to control the disease. It is urgent to explore biocontrol agents to control Foc TR4 and the secretion of mycotoxin. In this study, fluvirucin B6 was screened from Streptomyces solisilvae using an activity-guided method. Fluvirucin B6 exhibited strong antifungal activity against Foc TR4 (0.084 mM of EC50 value) and significantly inhibited mycelial growth and spore germination. Further studies demonstrated that fluvirucin B6 could cause the functional loss of mitochondria, the disorder of metabolism of Foc TR4 cells, and the decrease of enzyme activities in the tricarboxylic acid cycle and electron transport chain, ultimately inhibiting mycotoxin metabolism. In a pot experiment, the application of fluvirucin B6 significantly decreased the incidence of banana Fusarium wilt and the amount of Foc TR4 and controlled fungal toxins in the soil. Additionally, fluvirucin B6 could positively regulate the changes in the structure of the banana rhizosphere microbial community, significantly enriching beneficial microbes associated with disease resistance. In summary, this study identifies fluvirucin B6, which plays versatile roles in managing fungal diseases and mycotoxins.
Collapse
Affiliation(s)
- Yufeng Chen
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - XiaoJuan Li
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengbo Zhou
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yongzan Wei
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Junting Feng
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Bingyu Cai
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Dengfeng Qi
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Miaoyi Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yankun Zhao
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kai Li
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Zhiqiang Pan
- Agricultural Research Service, Natural Products Utilization Research Unit, U.S. Department of Agriculture, University of Mississippi, University, Mississippi 38677, United States
| | - Wei Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Jianghui Xie
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| |
Collapse
|
3
|
Candeliere F, Sola L, Busi E, Rossi M, Amaretti A, Raimondi S. The Metabolism of Leuconostoc Genus Decoded by Comparative Genomics. Microorganisms 2024; 12:1487. [PMID: 39065255 PMCID: PMC11279345 DOI: 10.3390/microorganisms12071487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Leuconostoc encompasses a number of species that frequently appear in foods where they play different roles, ranging from ripening to spoiling. The number of available Leuconostoc genomes has recently increased and enabled the precise taxonomic and phylogenetic delineation of species. Nonetheless, a thorough investigation of the functions and the metabolic potential of Leuconostoc species has never been accomplished. In this study, all the currently available 553 Leuconostoc genomes were downloaded from NCBI GenBank and annotated utilizing specific tools in order to reconstruct the metabolic potential of the genus in terms of carbohydrate hydrolysis and fermentative pathways, transporters, and anabolic potential. The analysis revealed that species cluster based on their metabolic potential, showing unique adaptation and ecological roles. Pentose phosphate and phosphoketolase pathways were highlighted as the main ones of central metabolism. The various identified PTS and ABC transporters showed adaptability to different sugars. The metabolic diversity described in this study not only supports the role of Leuconostoc spp. in natural ecosystems but also highlights their potential in industrial applications, particularly in the fermentation industry where their ability to metabolize a wide range of substrates can be harnessed for the production of various fermented foods and bioproducts.
Collapse
Affiliation(s)
- Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.C.); (L.S.); (E.B.); (M.R.)
| | - Laura Sola
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.C.); (L.S.); (E.B.); (M.R.)
| | - Enrico Busi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.C.); (L.S.); (E.B.); (M.R.)
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.C.); (L.S.); (E.B.); (M.R.)
- Biogest-Siteia, University of Modena and Reggio Emilia, 42124 Reggio Emilia, Italy
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.C.); (L.S.); (E.B.); (M.R.)
- Biogest-Siteia, University of Modena and Reggio Emilia, 42124 Reggio Emilia, Italy
| | - Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (F.C.); (L.S.); (E.B.); (M.R.)
- Biogest-Siteia, University of Modena and Reggio Emilia, 42124 Reggio Emilia, Italy
| |
Collapse
|
4
|
Wang Z, Li N, Xu Y, Wang W, Liu Y. Functional activity of endophytic bacteria G9H01 with high salt tolerance and anti-Magnaporthe oryzae that isolated from saline-alkali-tolerant rice. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171822. [PMID: 38521266 DOI: 10.1016/j.scitotenv.2024.171822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/24/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
It holds significant practical importance to screen and investigate endophytic bacteria with salt-tolerant activity in rice for the development of relevant microbial agents. A total of 179 strains of endophytic bacteria were isolated from 24 samples of salt-tolerant rice seeds, with almost 95 % of these bacteria exhibiting tolerance to a salt content of 2 % (0.34 mol/L). Following the screening process, a bacterium named G9H01 was identified, which demonstrated a salt tolerance of up to 15 % (2.57 mol/L) and resistance to Magnaporthe oryzae, the causal agent of rice blast disease. Phylogenetic analysis confirmed G9H01 as a strain of Bacillus paralicheniformis. The complete genome of G9H01 was sequenced and assembled, revealing a considerable number of genes encoding proteins associated with salt tolerance. Further analysis indicated that G9H01 may alleviate salt stress in a high-salt environment through various mechanisms. These mechanisms include the utilization of proteins such as K+ transporters, antiporters, and Na+/H+ antiporters, which are involved in K+ absorption and Na+ excretion. G9H01 also demonstrated the ability to uptake and accumulate betaine, as well as secrete extracellular polysaccharides. Collectively, these findings suggest that Bacillus paralicheniformis G9H01 has potential as a biocontrol agent, capable of promoting rice growth under saline-alkali-tolerant conditions.
Collapse
Affiliation(s)
- Zhishan Wang
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Ni Li
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha 410125, China
| | - Youqiang Xu
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China.
| | - Weiping Wang
- State Key Laboratory of Hybrid Rice (Hunan Hybrid Rice Research Center), Changsha 410125, China.
| | - Yang Liu
- School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China.
| |
Collapse
|
5
|
Feng Y, Arsenault D, Louyakis AS, Altman-Price N, Gophna U, Papke RT, Gogarten JP. Using the pan-genomic framework for the discovery of genomic islands in the haloarchaeon Halorubrum ezzemoulense. mBio 2024; 15:e0040824. [PMID: 38619241 PMCID: PMC11078007 DOI: 10.1128/mbio.00408-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 03/19/2024] [Indexed: 04/16/2024] Open
Abstract
In this study, we use pan-genomics to characterize the genomic variability of the widely dispersed halophilic archaeal species Halorubrum ezzemoulense (Hez). We include a multi-regional sampling of newly sequenced, high-quality draft genomes. The pan-genome graph of the species reveals 50 genomic islands that represent rare accessory genetic capabilities available to members. Most notably, we observe rearrangements that have led to the insertion/recombination/replacement of mutually exclusive genomic islands in equivalent genome positions ("homeocassettes"). These conflicting islands encode for similar functions, but homologs from islands located between the same core genes exhibit high divergence on the amino acid level, while the neighboring core genes are nearly identical. Both islands of a homeocassette often coexist in the same geographic location, suggesting that either island may be beyond the reach of selective sweeps and that these loci of divergence between Hez members are maintained and persist long term. This implies that subsections of the population have different niche preferences and rare metabolic capabilities. After an evaluation of the gene content in the homeocassettes, we speculate that these islands may play a role in the speciation, niche adaptability, and group selection dynamics in Hez. Though homeocassettes are first described in this study, similar replacements and divergence of genes on genomic islands have been previously reported in other Haloarchaea and distantly related Archaea, suggesting that homeocassettes may be a feature in a wide range of organisms outside of Hez.IMPORTANCEThis study catalogs the rare genes discovered in strains of the species Halorubrum ezzemoulense (Hez), an obligate halophilic archaeon, through the perspective of its pan-genome. These rare genes are often found to be arranged on islands that confer metabolic and transport functions and contain genes that have eluded previous studies. The discovery of divergent, but homologous islands occupying equivalent genome positions ("homeocassettes") in different genomes, reveals significant new information on genome evolution in Hez. Homeocassette pairs encode for similar functions, but their dissimilarity and distribution imply high rates of recombination, different specializations, and niche preferences in Hez. The coexistence of both islands of a homeocassette pair in multiple environments demonstrates that both islands are beyond the reach of selective sweeps and that these genome content differences between strains persist long term. The switch between islands through recombination under different environmental conditions may lead to a greater range of niche adaptability in Hez.
Collapse
Affiliation(s)
- Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Danielle Arsenault
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Artemis S. Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Neta Altman-Price
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Avinoam Adam Department of Natural Sciences, The Open University of Israel, Raanana, Israel
| | - Uri Gophna
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - R. Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|
6
|
van Lill M, Venter SN, Muema EK, Palmer M, Chan WY, Beukes CW, Steenkamp ET. SeqCode facilitates naming of South African rhizobia left in limbo. Syst Appl Microbiol 2024; 47:126504. [PMID: 38593622 DOI: 10.1016/j.syapm.2024.126504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa's current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.
Collapse
Affiliation(s)
- Melandré van Lill
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| | - Stephanus N Venter
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Esther K Muema
- Department of Soil Science, Faculty of AgriSciences, Stellenbosch University, South Africa
| | - Marike Palmer
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Wai Y Chan
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | | | - Emma T Steenkamp
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.
| |
Collapse
|
7
|
Mussig AJ, Chaumeil PA, Chuvochina M, Rinke C, Parks DH, Hugenholtz P. Putative genome contamination has minimal impact on the GTDB taxonomy. Microb Genom 2024; 10:001256. [PMID: 38809778 PMCID: PMC11261887 DOI: 10.1099/mgen.0.001256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
The Genome Taxonomy Database (GTDB) provides a species to domain classification of publicly available genomes based on average nucleotide identity (ANI) (for species) and a concatenated gene phylogeny normalized by evolutionary rates (for genus to phylum), which has been widely adopted by the scientific community. Here, we use the Genome UNClutterer (GUNC) software to identify putatively contaminated genomes in GTDB release 07-RS207. We found that GUNC reported 35,723 genomes as putatively contaminated, comprising 11.25 % of the 317,542 genomes in GTDB release 07-RS207. To assess the impact of this high level of inferred contamination on the delineation of taxa, we created 'clean' versions of the 34,846 putatively contaminated bacterial genomes by removing the most contaminated half. For each clean half, we re-calculated the ANI and concatenated gene phylogeny and found that only 77 (0.22 %) of the genomes were not consistent with their original classification. We conclude that the delineation of taxa in GTDB is robust to the putative contamination detected by GUNC.
Collapse
Affiliation(s)
- Aaron J. Mussig
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Pierre-Alain Chaumeil
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Maria Chuvochina
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Christian Rinke
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Donovan H. Parks
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| | - Philip Hugenholtz
- The University of Queensland, School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, St Lucia, QLD, Australia
| |
Collapse
|
8
|
Wu R, Payne M, Zhang L, Lan R. Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses. mSystems 2024; 9:e0121823. [PMID: 38530055 PMCID: PMC11019964 DOI: 10.1128/msystems.01218-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Campylobacter species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the Campylobacter genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the Campylobacter genus core genome (500 loci) using publicly available Campylobacter complete genomes (n = 498) and constructed a core genome phylogeny using 2,193 publicly available Campylobacter genomes to examine inter-species diversity and species boundaries. Utilizing 8,440 Campylobacter genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated Campylobacter species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had in silico DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool Campylobacter Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%. The ANI genomic species definitions proposed here allow consistent species definition in the Campylobacter genus and will facilitate the detection of novel species in the future.IMPORTANCEIn recent years, Campylobacter has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the Campylobacter genus in public databases. Currently, a standardized Campylobacter species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the Campylobacter genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the Campylobacter species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed Campylobacter Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to Campylobacter genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus Campylobacter.
Collapse
Affiliation(s)
- Ruochen Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
9
|
Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74. [PMID: 38512750 DOI: 10.1099/ijsem.0.006300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024] Open
Abstract
The field of microbial taxonomy is dynamic, aiming to provide a stable and contemporary classification system for prokaryotes. Traditionally, reliance on phenotypic characteristics limited the comprehensive understanding of microbial diversity and evolution. The introduction of molecular techniques, particularly DNA sequencing and genomics, has transformed our perception of prokaryotic diversity. In the past two decades, advancements in genome sequencing have transitioned from traditional methods to a genome-based taxonomic framework, not only to define species, but also higher taxonomic ranks. As technology and databases rapidly expand, maintaining updated standards is crucial. This work seeks to revise the 2018 guidelines for applying genome sequencing data in microbial taxonomy, adapting minimal standards and recommendations to reflect technological progress during this period.
Collapse
Affiliation(s)
- Raúl Riesco
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, Queensland, Australia
| | - Martha E Trujillo
- Departamento de Microbiología y Genética, Campus Miguel de Unamuno, University of Salamanca, 37007 Salamanca, Spain
| |
Collapse
|
10
|
Rossi FPN, Flores VS, Uceda-Campos G, Amgarten DE, Setubal JC, da Silva AM. Comparative Analyses of Bacteriophage Genomes. Methods Mol Biol 2024; 2802:427-453. [PMID: 38819567 DOI: 10.1007/978-1-0716-3838-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Bacterial viruses (bacteriophages or phages) are the most abundant and diverse biological entities on Earth. There is a renewed worldwide interest in phage-centered research motivated by their enormous potential as antimicrobials to cope with multidrug-resistant pathogens. An ever-growing number of complete phage genomes are becoming available, derived either from newly isolated phages (cultivated phages) or recovered from metagenomic sequencing data (uncultivated phages). Robust comparative analysis is crucial for a comprehensive understanding of genotypic variations of phages and their related evolutionary processes, and to investigate the interaction mechanisms between phages and their hosts. In this chapter, we present a protocol for phage comparative genomics employing tools selected out of the many currently available, focusing on complete genomes of phages classified in the class Caudoviricetes. This protocol provides accurate identification of similarities, differences, and patterns among new and previously known complete phage genomes as well as phage clustering and taxonomic classification.
Collapse
Affiliation(s)
| | - Vinicius Sousa Flores
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Guillermo Uceda-Campos
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | | | - João Carlos Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil
| | - Aline Maria da Silva
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Sao Paulo, SP, Brazil.
| |
Collapse
|
11
|
Luo Z, Ning Y, Yu S, Xiao M, Dai R, Chen X, Wang Y, Kang W, Jiang Y, Yu H, Liang H, Xu Y, Sun T, Zhang L. The first established microsatellite markers to distinguish Candida orthopsilosis isolates and detection of a nosocomial outbreak in China. J Clin Microbiol 2023; 61:e0080623. [PMID: 37877725 PMCID: PMC10662339 DOI: 10.1128/jcm.00806-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Abstract
The infection proportion of Candida orthopsilosis, a member of the C. parapsilosis complex, has increased globally in recent years, and nosocomial outbreaks have been reported in several countries. This study aimed to establish microsatellite loci-based typing method that was able to effectively distinguish among C. orthopsilosis isolates. Three reference C. orthopsilosis genome sequences were analyzed to identify repeat loci. DNA sequences containing over eight bi- or more nucleotide repeats were selected. A total of 51 loci were initially identified, and locus-specific primers were designed and tested with 20 epidemiologically unrelated isolates. Four loci with excellent reproducibility, specificity, and resolution for molecular typing purposes were identified, and the combined discriminatory power (DP, based on 20 epidemiologically unrelated isolates) of these four loci was 1.0. Reproducibility was demonstrated by consistently testing three strains each in triplicate, and stability, demonstrated by testing 10 successive passages. Then, we collected 48 C. orthopsilosis non-duplicate clinical isolates from the China Hospital Invasive Fungal Surveillance Net study to compare the DP of the microsatellite-based typing with internal transcribed spacer (ITS) and amplified fragment length polymorphism (AFLP) typing analyses, using ATCC 96139 as a reference strain. These 49 isolates were subdivided into 12 microsatellite types (COMT1-12), six AFLP types, and three ITS types, while all the isolates with the same COMT belonged to consistent AFLP and ITS type, demonstrating the high DP of our microsatellite-type method. According to our results, COMT12 was found to be the predominant type in China, and COMT5 was the second largest and responsible for causing a nosocomial outbreak. This microsatellite-type method is a valuable tool for the differentiation of C. orthopsilosis and could be vital for epidemiological studies to determine strain relatedness and monitor transmission.
Collapse
Affiliation(s)
- Zhengyu Luo
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yating Ning
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Graduate School, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Shuying Yu
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Meng Xiao
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Rongchen Dai
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinfei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yao Wang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Wei Kang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yan Jiang
- Department of Microbiology and Immunology, Guizhou Medical University Affiliated Hospital, Guiyang, China
| | - Hua Yu
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongjie Liang
- Department of Clinical Laboratory, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Tianshu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
- Clinical Biobank, Medical Research Center, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| |
Collapse
|
12
|
Alioto TS, Gut M, Rodiño-Janeiro BK, Cruz F, Gómez-Garrido J, Vázquez-Ucha JC, Mata C, Antoni R, Briansó F, Dabad M, Casals E, Ingham M, Álvarez-Tejado M, Bou G, Gut IG. Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales. Microb Genom 2023; 9. [PMID: 38010338 DOI: 10.1099/mgen.0.001132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
In response to the threat of increasing antimicrobial resistance, we must increase the amount of available high-quality genomic data gathered on antibiotic-resistant bacteria. To this end, we developed an integrated pipeline for high-throughput long-read sequencing, assembly, annotation and analysis of bacterial isolates and used it to generate a large genomic data set of carbapenemase-producing Enterobacterales (CPE) isolates collected in Spain. The set of 461 isolates were sequenced with a combination of both Illumina and Oxford Nanopore Technologies (ONT) DNA sequencing technologies in order to provide genomic context for chromosomal loci and, most importantly, structural resolution of plasmids, important determinants for transmission of antimicrobial resistance. We developed an informatics pipeline called Assembly and Annotation of Carbapenem-Resistant Enterobacteriaceae (AACRE) for the full assembly and annotation of the bacterial genomes and their complement of plasmids. To explore the resulting genomic data set, we developed a new database called inCREDBle that not only stores the genomic data, but provides unique ways to filter and compare data, enabling comparative genomic analyses at the level of chromosomes, plasmids and individual genes. We identified a new sequence type, ST5000, and discovered a genomic locus unique to ST15 that may be linked to its increased spread in the population. In addition to our major objective of generating a large regional data set, we took the opportunity to compare the effects of sample quality and sequencing methods, including R9 versus R10 nanopore chemistry, on genome assembly and annotation quality. We conclude that converting short-read and hybrid microbial sequencing and assembly workflows to the latest nanopore chemistry will further reduce processing time and cost, truly enabling the routine monitoring of resistance transmission patterns at the resolution of complete chromosomes and plasmids.
Collapse
Affiliation(s)
- Tyler S Alioto
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Marta Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Bruno Kotska Rodiño-Janeiro
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
| | - Fernando Cruz
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Jèssica Gómez-Garrido
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Juan Carlos Vázquez-Ucha
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Caterina Mata
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Regina Antoni
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Ferran Briansó
- Department of Genetics, Microbiology and Statistics, Universitat de Barcelona (UB), Barcelona, Spain
- Roche Diagnostics, Sant Cugat del Vallès, Barcelona, Spain
| | - Marc Dabad
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Eloi Casals
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | - Matthew Ingham
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| | | | - Germán Bou
- Microbiology Department, Complejo Hospitalario Universitario A Coruña-Instituto Investigación Biomédica A Coruña (INIBIC), A Coruña, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat de Barcelona (UB), Barcelona, Spain
| |
Collapse
|
13
|
Shikov AE, Merkushova AV, Savina IA, Nizhnikov AA, Antonets KS. The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome. Front Microbiol 2023; 14:1211999. [PMID: 38029097 PMCID: PMC10656689 DOI: 10.3389/fmicb.2023.1211999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors. Methods We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants. Results According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively. Discussion In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.
Collapse
Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Anastasiya V. Merkushova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| |
Collapse
|
14
|
Rodrigues Jardim B, Tran-Nguyen LTT, Gambley C, Al-Sadi AM, Al-Subhi AM, Foissac X, Salar P, Cai H, Yang JY, Davis R, Jones L, Rodoni B, Constable FE. The observation of taxonomic boundaries for the 16SrII and 16SrXXV phytoplasmas using genome-based delimitation. Int J Syst Evol Microbiol 2023; 73. [PMID: 37486824 DOI: 10.1099/ijsem.0.005977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
Within the 16SrII phytoplasma group, subgroups A-X have been classified based on restriction fragment length polymorphism of their 16S rRNA gene, and two species have been described, namely 'Candidatus Phytoplasma aurantifolia' and 'Ca. Phytoplasma australasia'. Strains of 16SrII phytoplasmas are detected across a broad geographic range within Africa, Asia, Australia, Europe and North and South America. Historically, all members of the 16SrII group share ≥97.5 % nucleotide sequence identity of their 16S rRNA gene. In this study, we used whole genome sequences to identify the species boundaries within the 16SrII group. Whole genome analyses were done using 42 phytoplasma strains classified into seven 16SrII subgroups, five 16SrII taxa without official 16Sr subgroup classifications, and one 16SrXXV-A phytoplasma strain used as an outgroup taxon. Based on phylogenomic analyses as well as whole genome average nucleotide and average amino acid identity (ANI and AAI), eight distinct 16SrII taxa equivalent to species were identified, six of which are novel descriptions. Strains within the same species had ANI and AAI values of >97 %, and shared ≥80 % of their genomic segments based on the ANI analysis. Species also had distinct biological and/or ecological features. A 16SrII subgroup often represented a distinct species, e.g., the 16SrII-B subgroup members. Members classified within the 16SrII-A, 16SrII-D, and 16SrII-V subgroups as well as strains classified as sweet potato little leaf phytoplasmas fulfilled criteria to be included as members of a single species, but with subspecies-level relationships with each other. The 16SrXXV-A taxon was also described as a novel phytoplasma species and, based on criteria used for other bacterial families, provided evidence that it could be classified as a distinct genus from the 16SrII phytoplasmas. As more phytoplasma genome sequences become available, the classification system of these bacteria can be further refined at the genus, species, and subspecies taxonomic ranks.
Collapse
Affiliation(s)
- Bianca Rodrigues Jardim
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | | | - Cherie Gambley
- Horticulture and Forestry Science, Department of Agriculture and Fisheries Maroochy Research Facility, Nambour, Queensland, Australia
| | - Abdullah M Al-Sadi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ali M Al-Subhi
- Department of Plant Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - Xavier Foissac
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Pascal Salar
- University of Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, 33140, Bordeaux, Villenave d'Ornon, France
| | - Hong Cai
- The Key Laboratory for Plant Pathology, Yunnan Agricultural University, Kunming 650201, PR China
| | - Jun-Yi Yang
- Institute of Biochemistry, National Chung Hsing University, Taichung 402, Taiwan, ROC
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan, ROC
| | - Richard Davis
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Lynne Jones
- Northern Australia Quarantine Strategy, Department of Agriculture, Fisheries and Forestry, Canberra, Australian Capital Territory 2601, Australia
| | - Brendan Rodoni
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| | - Fiona E Constable
- School of Applied Systems Biology, La Trobe University, Bundoora, Victoria, Australia
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Bundoora, Victoria, Australia
| |
Collapse
|
15
|
An J, Zhang Y, Zhao Z, Huan R, Yi H, Wang H, Luan C, Feng S, Huang H, Li S, Wang D, Zhai Z, Hao Y. Molecular Organization and Functional Analysis of a Novel Plasmid-Borne cps Gene Cluster from Lactiplantibacillus plantarum YC41. Microbiol Spectr 2023; 11:e0415022. [PMID: 36877018 PMCID: PMC10100969 DOI: 10.1128/spectrum.04150-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/03/2023] [Indexed: 03/07/2023] Open
Abstract
Capsular polysaccharide (CPS) can tightly attach to bacterial surfaces and plays a critical role in protecting microorganisms from environmental stresses. However, the molecular and functional properties of some plasmid-borne cps gene clusters are poorly understood. In this study, comparative genomics of the draft genomes of 21 Lactiplantibacillus plantarum strains revealed that the specific gene cluster for CPS biosynthesis was observed only in the 8 strains with a ropy phenotype. Furthermore, the complete genomes showed that the specific gene cluster cpsYC41 was located on the novel plasmid pYC41 in L. plantarum YC41. In silico analysis confirmed that the cpsYC41 gene cluster contained the dTDP-rhamnose precursor biosynthesis operon, the repeating-unit biosynthesis operon, and the wzx gene. The insertional inactivation of the rmlA and cpsC genes abolished the ropy phenotype and reduced the CPS yields by 93.79% and 96.62%, respectively, in L. plantarum YC41 mutants. These results revealed that the cpsYC41 gene cluster was responsible for CPS biosynthesis. Moreover, the survival rates of the YC41-rmlA- and YC41-cpsC- mutants under acid, NaCl, and H2O2 stresses were decreased by 56.47 to 93.67% compared to that of the control strain. Furthermore, the specific cps gene cluster was also confirmed to play a vital role in CPS biosynthesis in L. plantarum MC2, PG1, and YD2. These findings enhance our understanding of the genetic organization and gene functions of plasmid-borne cps gene clusters in L. plantarum. IMPORTANCE Capsular polysaccharide is well known to protect bacteria against various environmental stresses. The gene cluster for CPS biosynthesis is typically organized in the chromosome in bacteria. It is worth noting that complete genome sequencing showed that a novel plasmid pYC41-borne cpsYC41 gene cluster was identified in L. plantarum YC41. The cpsYC41 gene cluster included the dTDP-rhamnose precursor biosynthesis operon, the repeating-unit biosynthesis operon, and the wzx gene, which was verified by the significantly decreased CPS yield and the absent ropy phenotype in the corresponding mutants. The cpsYC41 gene cluster plays an important role in bacterial survival under environmental stress, and the mutants had decreased fitness under stress conditions. The vital role of this specific cps gene cluster in CPS biosynthesis was also confirmed in other CPS-producing L. plantarum strains. These results advanced a better understanding of the molecular mechanisms of plasmid-borne cps gene clusters and the protective functionality of CPS.
Collapse
Affiliation(s)
- Jieran An
- Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yuchen Zhang
- Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Zhaoer Zhao
- Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Ran Huan
- Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Huaxi Yi
- College of Food Science and Engineering, Ocean University of China, Qingdao, China
| | - Hui Wang
- Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Chunguang Luan
- China National Research Institute of Food and Fermentation Industries, Beijing, China
| | | | | | - Shanwen Li
- Qinghai Huzhu Barley Wine Co. Ltd., Haining, China
| | - Deliang Wang
- China National Research Institute of Food and Fermentation Industries, Beijing, China
| | - Zhengyuan Zhai
- Key Laboratory of Functional Dairy, Co-constructed by the Ministry of Education and Beijing Municipality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yanling Hao
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, China
| |
Collapse
|
16
|
Choi Y, Ahn S, Park M, Lee S, Cho S, Kim H. HGTree v2.0: a comprehensive database update for horizontal gene transfer (HGT) events detected by the tree-reconciliation method. Nucleic Acids Res 2022; 51:D1010-D1018. [PMID: 36350646 PMCID: PMC9825516 DOI: 10.1093/nar/gkac929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 09/30/2022] [Accepted: 11/01/2022] [Indexed: 11/11/2022] Open
Abstract
HGTree is a database that provides horizontal gene transfer (HGT) event information on 2472 prokaryote genomes using the tree-reconciliation method. HGTree was constructed in 2015, and a large number of prokaryotic genomes have been additionally published since then. To cope with the rapid rise of prokaryotic genome data, we present HGTree v2.0 (http://hgtree2.snu.ac.kr), a newly updated version of our HGT database with much more extensive data, including a total of 20 536 completely sequenced non-redundant prokaryotic genomes, and more reliable HGT information results curated with various steps. As a result, HGTree v2.0 has a set of expanded data results of 6 361 199 putative horizontally transferred genes integrated with additional functional information such as the KEGG pathway, virulence factors and antimicrobial resistance. Furthermore, various visualization tools in the HGTree v2.0 database website provide intuitive biological insights, allowing the users to investigate their genomes of interest.
Collapse
Affiliation(s)
| | | | - Myeongkyu Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | | | - Seoae Cho
- eGnome Inc., Seoul 05836, Republic of Korea
| | - Heebal Kim
- To whom correspondence should be addressed. Tel: +82 2 880 4803; Fax: +82 2 883 8812;
| |
Collapse
|
17
|
Gtari M. Taxogenomic status of phylogenetically distant Frankia clusters warrants their elevation to the rank of genus: A description of Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov. as three novel genera within the family Frankiaceae. Front Microbiol 2022; 13:1041425. [PMID: 36425027 PMCID: PMC9680954 DOI: 10.3389/fmicb.2022.1041425] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/12/2022] [Indexed: 11/10/2022] Open
Abstract
The genus Frankia is at present the sole genus in the family Frankiaceae and encompasses filamentous, sporangia-forming actinomycetes principally isolated from root nodules of taxonomically disparate dicotyledonous hosts named actinorhizal plants. Multiple independent phylogenetic analyses agree with the division of the genus Frankia into four well-supported clusters. Within these clusters, Frankia strains are well defined based on host infectivity range, mode of infection, morphology, and their behaviour in culture. In this study, phylogenomics, overall genome related indices (OGRI), together with available data sets for phenotypic and host-plant ranges available for the type strains of Frankia species, were considered. The robustness and the deep radiation observed in Frankia at the subgeneric level, fulfilling the primary principle of phylogenetic systematics, were strengthened by establishing genome criteria for new genus demarcation boundaries. Therefore, the taxonomic elevation of the Frankia clusters to the rank of the genus is proposed. The genus Frankia should be revised to encompass cluster 1 species only and three novel genera, Protofrankia gen. nov., Parafrankia gen. nov., and Pseudofrankia gen. nov., are proposed to accommodate clusters 2, 3, and 4 species, respectively. New combinations for validly named species are also provided.
Collapse
Affiliation(s)
- Maher Gtari
- USCR Bactériologie Moléculaire & Génomique, Institut National des Sciences Appliquées et de Technologie, Université de Carthage, Tunis, Tunisia
| |
Collapse
|
18
|
Raimondi S, Candeliere F, Amaretti A, Costa S, Vertuani S, Spampinato G, Rossi M. Phylogenomic analysis of the genus Leuconostoc. Front Microbiol 2022; 13:897656. [PMID: 35958134 PMCID: PMC9358442 DOI: 10.3389/fmicb.2022.897656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
Leuconostoc is a genus of saccharolytic heterofermentative lactic acid bacteria that inhabit plant-derived matrices and a variety of fermented foods (dairy products, dough, milk, vegetables, and meats), contributing to desired fermentation processes or playing a role in food spoilage. At present, the genus encompasses 17 recognized species. In total, 216 deposited genome sequences of Leuconostoc were analyzed, to check the delineation of species and to infer their evolutive genealogy utilizing a minimum evolution tree of Average Nucleotide Identity (ANI) and the core genome alignment. Phylogenomic relationships were compared to those obtained from the analysis of 16S rRNA, pheS, and rpoA genes. All the phylograms were subjected to split decomposition analysis and their topologies were compared to check the ambiguities in the inferred phylogenesis. The minimum evolution ANI tree exhibited the most similar topology with the core genome tree, while single gene trees were less adherent and provided a weaker phylogenetic signal. In particular, the 16S rRNA gene failed to resolve several bifurcations and Leuconostoc species. Based on an ANI threshold of 95%, the organization of the genus Leuconostoc could be amended, redefining the boundaries of the species L. inhae, L. falkenbergense, L. gelidum, L. lactis, L. mesenteroides, and L. pseudomesenteroides. Two strains currently recognized as L. mesenteroides were split into a separate lineage representing a putative species (G16), phylogenetically related to both L. mesenteroides (G18) and L. suionicum (G17). Differences among the four subspecies of L. mesenteroides were not pinpointed by ANI or by the conserved genes. The strains of L. pseudomesenteroides were ascribed to two putative species, G13 and G14, the former including also all the strains presently belonging to L. falkenbergense. L. lactis was split into two phylogenetically related lineages, G9 and G10, putatively corresponding to separate species and both including subgroups that may correspond to subspecies. The species L. gelidum and L. gasicomitatum were closely related but separated into different species, the latter including also L. inhae strains. These results, integrating information of ANI, core genome, and housekeeping genes, complemented the taxonomic delineation with solid information on the phylogenetic lineages evolved within the genus Leuconostoc.
Collapse
Affiliation(s)
- Stefano Raimondi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Francesco Candeliere
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Alberto Amaretti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Stefania Costa
- Department of Chemical, Pharmaceutical and Agricultural Sciences—DOCPAS, University of Ferrara, Ferrara, Italy
| | - Silvia Vertuani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Gloria Spampinato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Maddalena Rossi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Biogest Siteia, University of Modena and Reggio Emilia, Reggio Emilia, Italy
- *Correspondence: Maddalena Rossi
| |
Collapse
|
19
|
Feng Y, Neri U, Gosselin S, Louyakis AS, Papke RT, Gophna U, Gogarten JP. The Evolutionary Origins of Extreme Halophilic Archaeal Lineages. Genome Biol Evol 2021; 13:6320066. [PMID: 34255041 PMCID: PMC8350355 DOI: 10.1093/gbe/evab166] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2021] [Indexed: 12/12/2022] Open
Abstract
Interest and controversy surrounding the evolutionary origins of extremely halophilic Archaea has increased in recent years, due to the discovery and characterization of the Nanohaloarchaea and the Methanonatronarchaeia. Initial attempts in explaining the evolutionary placement of the two new lineages in relation to the classical Halobacteria (also referred to as Haloarchaea) resulted in hypotheses that imply the new groups share a common ancestor with the Haloarchaea. However, more recent analyses have led to a shift: the Nanohaloarchaea have been largely accepted as being a member of the DPANN superphylum, outside of the euryarchaeota; whereas the Methanonatronarchaeia have been placed near the base of the Methanotecta (composed of the class II methanogens, the Halobacteriales, and Archaeoglobales). These opposing hypotheses have far-reaching implications on the concepts of convergent evolution (distantly related groups evolve similar strategies for survival), genome reduction, and gene transfer. In this work, we attempt to resolve these conflicts with phylogenetic and phylogenomic data. We provide a robust taxonomic sampling of Archaeal genomes that spans the Asgardarchaea, TACK Group, euryarchaeota, and the DPANN superphylum. In addition, we assembled draft genomes from seven new representatives of the Nanohaloarchaea from distinct geographic locations. Phylogenies derived from these data imply that the highly conserved ATP synthase catalytic/noncatalytic subunits of Nanohaloarchaea share a sisterhood relationship with the Haloarchaea. We also employ a novel gene family distance clustering strategy which shows this sisterhood relationship is not likely the result of a recent gene transfer. In addition, we present and evaluate data that argue for and against the monophyly of the DPANN superphylum, in particular, the inclusion of the Nanohaloarchaea in DPANN.
Collapse
Affiliation(s)
- Yutian Feng
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Neri
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Sean Gosselin
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Artemis S Louyakis
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - R Thane Papke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA
| | - Uri Gophna
- Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Israel
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, USA.,Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut, USA
| |
Collapse
|