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Schulz T, Parmigiani L, Rempel A, Stoye J. Methods for Pangenomic Core Detection. Methods Mol Biol 2024; 2802:73-106. [PMID: 38819557 DOI: 10.1007/978-1-0716-3838-5_4] [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
Computational pangenomics deals with the joint analysis of all genomic sequences of a species. It has already been successfully applied to various tasks in many research areas. Further advances in DNA sequencing technologies constantly let more and more genomic sequences become available for many species, leading to an increasing attractiveness of pangenomic studies. At the same time, larger datasets also pose new challenges for data structures and algorithms that are needed to handle the data. Efficient methods oftentimes make use of the concept of k-mers.Core detection is a common way of analyzing a pangenome. The pangenome's core is defined as the subset of genomic information shared among all individual members. Classically, it is not only determined on the abstract level of genes but can also be described on the sequence level.In this chapter, we provide an overview of k-mer-based methods in the context of pangenomics studies. We first revisit existing software solutions for k-mer counting and k-mer set representation. Afterward, we describe the usage of two k-mer-based approaches, Pangrowth and Corer, for pangenomic core detection.
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Affiliation(s)
- Tizian Schulz
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Luca Parmigiani
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Andreas Rempel
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jens Stoye
- Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.
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2
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Crosby WB, Karisch BB, Hiott LM, Pinnell LJ, Pittman A, Frye JG, Jackson CR, Loy JD, Epperson WB, Blanton J, Capik SF, Morley PS, Woolums AR. Tulathromycin metaphylaxis increases nasopharyngeal isolation of multidrug resistant Mannheimia haemolytica in stocker heifers. Front Vet Sci 2023; 10:1256997. [PMID: 38053814 PMCID: PMC10694364 DOI: 10.3389/fvets.2023.1256997] [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: 07/11/2023] [Accepted: 10/25/2023] [Indexed: 12/07/2023] Open
Abstract
Bovine respiratory disease (BRD) is a leading cause of disease in feedlot and stocker calves with Mannheimia haemolytica (MH) as one of the most common etiologies. One of the most effective means of controlling BRD is through metaphylaxis, which involves administering antimicrobials to all animals at high risk of developing BRD. However, increasing prevalence of multidrug resistant (MDR) MH may reduce efficacy of metaphylaxis due to decreased susceptibility to drugs used for metaphylaxis. Primarily, this study aimed to determine the effect of tulathromycin metaphylaxis and subsequent BRD treatment on antimicrobial resistance (AMR) in MH isolated from stocker calves. Secondary objectives included evaluating the effect of metaphylaxis and treatment for BRD on animal health and comparing the genetic relationship of MH isolated. Crossbred beef heifers (n = 331, mean weight = 232, SD = 17.8 kg) at high risk for BRD were randomly assigned to receive tulathromycin metaphylaxis (META, n = 167) or not (NO META, n = 164). Nasopharyngeal swabs were collected for MH isolation, antimicrobial susceptibility testing and whole genome sequencing at arrival and 3 (WK3) and 10 (WK10) weeks later. Mixed-effects logistic regression was used to identify risk factors for isolation of MH and MDR MH (resistant to ≥3 antimicrobial drug classes) at 3 and 10 weeks, BRD morbidity, and crude mortality. Animals in the META group had higher odds of isolation of MDR MH at 3 weeks [OR (95% CI) = 13.08 (5-30.9), p < 0.0001] and 10 weeks [OR (95% CI) = 5.92 (1.34-26.14), p = 0.019] after arrival. There was no difference in risk of isolation of any MH (resistant or susceptible) between META and NO META groups at all timepoints. Animals in the NO META group had 3 times higher odds of being treated for BRD [WK3: OR (95% CI) = 3.07 (1.70-5.52), p = 0.0002; WK10: OR (95% CI) = 2.76 (1.59-4.80), p = 0.0002]. Antimicrobial resistance genes found within isolates were associated with integrative conjugative element (ICE) genes. Tulathromycin metaphylaxis increased risk of isolation of MDR MH and in this population, the increase in MDR MH appeared to be associated with ICE containing antimicrobial resistance genes for multiple antimicrobial classes. This may have important implications for future efficacy of antimicrobials for control and treatment of BRD.
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Affiliation(s)
- William B. Crosby
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - Brandi B. Karisch
- Department of Animal and Dairy Sciences, College of Agriculture and Life Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Lari M. Hiott
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, United States Department of Agriculture-Agricultural Research Service, Athens, GA, United States
| | - Lee J. Pinnell
- VERO Program, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX, United States
| | - Alexandra Pittman
- Department of Animal and Dairy Sciences, College of Agriculture and Life Sciences, Mississippi State University, Mississippi State, MS, United States
| | - Jonathan G. Frye
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, United States Department of Agriculture-Agricultural Research Service, Athens, GA, United States
| | - Charlene R. Jackson
- Poultry Microbiological Safety and Processing Research Unit, U.S. National Poultry Research Center, United States Department of Agriculture-Agricultural Research Service, Athens, GA, United States
| | - John Dustin Loy
- Nebraska Veterinary Diagnostic Center, School of Veterinary Medicine and Biomedical Sciences, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - William B. Epperson
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
| | - John Blanton
- Department of Animal Sciences, College of Agriculture, Purdue University, West Lafayette, IN, United States
| | - Sarah F. Capik
- Tumbleweed Veterinary Services, PLLC, Amarillo, TX, United States
| | - Paul S. Morley
- VERO Program, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, Canyon, TX, United States
| | - Amelia R. Woolums
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, Mississippi State, MS, United States
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Laux M, Piroupo CM, Setubal JC, Giani A. The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade. HARMFUL ALGAE 2023; 129:102518. [PMID: 37951618 DOI: 10.1016/j.hal.2023.102518] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/15/2023] [Accepted: 09/28/2023] [Indexed: 11/14/2023]
Abstract
Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.
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Affiliation(s)
- Marcele Laux
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil
| | - Carlos Morais Piroupo
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo, 05508-000, São Paulo, SP, Brazil
| | - Alessandra Giani
- Department of Botany, Phycology Laboratory, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil.
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Otero-Ruiz A, Rodriguez-Anaya LZ, Lares-Villa F, Lozano Aguirre Beltrán LF, Lares-Jiménez LF, Gonzalez-Galaviz JR, Cruz-Mendívil A. Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes. Sci Rep 2023; 13:14318. [PMID: 37653073 PMCID: PMC10471605 DOI: 10.1038/s41598-023-41657-6] [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: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023] Open
Abstract
Balamuthia mandrillaris is a pathogenic protozoan that causes a rare but almost always fatal infection of the central nervous system and, in some cases, cutaneous lesions. Currently, the genomic data for this free-living amoeba include the description of several complete mitochondrial genomes. In contrast, two complete genomes with draft quality are available in GenBank, but none of these have a functional annotation. In the present study, the complete genome of B. mandrillaris isolated from a freshwater artificial lagoon was sequenced and assembled, obtaining an assembled genome with better assembly quality parameter values than the currently available genomes. Afterward, the genome mentioned earlier, along with strains V039 and 2046, were subjected to functional annotation. Finally, comparative genomics analysis was performed, and it was found that homologous genes in the core genome potentially involved in the virulence of Acanthamoeba spp. and Trypanosoma cruzi. Moreover, eleven of fifteen genes were identified in the three strains described as potential target genes to develop new treatment approaches for B. mandrillaris infections. These results describe proteins in this protozoan's complete genome and help prioritize which target genes could be used to develop new treatments.
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Affiliation(s)
- Alejandro Otero-Ruiz
- Programa de Doctorado en Ciencias Especialidad en Biotecnología, Departamento de Biotecnología y Ciencias Alimentarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | - Luis Fernando Lozano Aguirre Beltrán
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas de la Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, 85000, Ciudad Obregón, Sonora, Mexico
| | | | - Abraham Cruz-Mendívil
- CONAHCYT-Instituto Politécnico Nacional, CIIDIR Unidad Sinaloa, 81101, Guasave, Sinaloa, Mexico
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Bing RG, Willard DJ, Crosby JR, Adams MWW, Kelly RM. Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype. Front Microbiol 2023; 14:1212538. [PMID: 37601363 PMCID: PMC10434631 DOI: 10.3389/fmicb.2023.1212538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 07/20/2023] [Indexed: 08/22/2023] Open
Abstract
The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, United States
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Tran TH, Roberts AQ, Escapa IF, Gao W, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Julie A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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Gao P, Zhang X, Huang X, Chen Z, Marietou A, Holmkvist L, Qu L, Finster K, Gong X. Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling. BMC Genomics 2023; 24:209. [PMID: 37076818 PMCID: PMC10116758 DOI: 10.1186/s12864-023-09297-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/04/2023] [Indexed: 04/21/2023] Open
Abstract
BACKGROUND Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen. RESULTS Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited. CONCLUSIONS Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.
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Affiliation(s)
- Ping Gao
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Xiaoting Zhang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Xiaomei Huang
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Zhiyi Chen
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China
| | - Angeliki Marietou
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Department of Biological and Chemical Engineering, Aarhus University, 8000, Aarhus, Denmark
| | - Lars Holmkvist
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
| | - Lingyun Qu
- Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources (MNR), 266061, Qingdao, PR China
- Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, 266237, Qingdao, PR China
| | - Kai Finster
- Section for Microbiology, Department of Biology, Aarhus University, 8000, Aarhus, Denmark
- Stellar Astrophysics Center, Department of Physics and Astronomy, Aarhus University, 8000, Aarhus, Denmark
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, 266237, Qingdao, PR China.
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Bing RG, Willard DJ, Manesh MJH, Laemthong T, Crosby JR, Adams MWW, Kelly RM. Complete Genome Sequences of Two Thermophilic Indigenous Bacteria Isolated from Wheat Straw, Thermoclostridium stercorarium subsp. Strain RKWS1 and Thermoanaerobacter sp. Strain RKWS2. Microbiol Resour Announc 2023; 12:e0119322. [PMID: 36749042 PMCID: PMC10019256 DOI: 10.1128/mra.01193-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/24/2023] [Indexed: 02/08/2023] Open
Abstract
Reported here are complete genome sequences for two anaerobic, thermophilic bacteria isolated from wheat straw, i.e., the (hemi)cellulolytic Thermoclostridium stercorarium subspecies strain RKWS1 (3,029,933 bp) and the hemicellulolytic Thermoanaerobacter species strain RKWS2 (2,827,640 bp). Discovery of indigenous thermophiles in plant biomass suggests that high-temperature microorganisms are more ubiquitous than previously thought.
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Affiliation(s)
- Ryan G. Bing
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Daniel J. Willard
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Mohamad J. H. Manesh
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Tunyaboon Laemthong
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - James R. Crosby
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | - Michael W. W. Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Robert M. Kelly
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
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Davis P, Seto D, Mahadevan P. CoreGenes5.0: An Updated User-Friendly Webserver for the Determination of Core Genes from Sets of Viral and Bacterial Genomes. Viruses 2022; 14:v14112534. [PMID: 36423143 PMCID: PMC9693508 DOI: 10.3390/v14112534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
The determination of core genes in viral and bacterial genomes is crucial for a better understanding of their relatedness and for their classification. CoreGenes5.0 is an updated user-friendly web-based software tool for the identification of core genes in and data mining of viral and bacterial genomes. This tool has been useful in the resolution of several issues arising in the taxonomic analysis of bacteriophages and has incorporated many suggestions from researchers in that community. The webserver displays result in a format that is easy to understand and allows for automated batch processing, without the need for any user-installed bioinformatics software. CoreGenes5.0 uses group protein clustering of genomes with one of three algorithm options to output a table of core genes from the input genomes. Previously annotated "unknown genes" may be identified with homologues in the output. The updated version of CoreGenes is able to handle more genomes, is faster, and is more robust, providing easier analysis of custom or proprietary datasets. CoreGenes5.0 is accessible at coregenes.org, migrating from a previous site.
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Affiliation(s)
- Patrick Davis
- Department of Biology, The University of Tampa, Tampa, FL 33606, USA
| | - Donald Seto
- Department of Systems Biology, George Mason University, Manassas, VA 20110, USA
- Correspondence: (D.S.); (P.M.)
| | - Padmanabhan Mahadevan
- Department of Biology, The University of Tampa, Tampa, FL 33606, USA
- Correspondence: (D.S.); (P.M.)
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Deb S. Pan-genome evolution and its association with divergence of metabolic functions in Bifidobacterium genus. World J Microbiol Biotechnol 2022; 38:231. [PMID: 36205822 DOI: 10.1007/s11274-022-03430-1] [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: 06/02/2022] [Accepted: 09/30/2022] [Indexed: 10/10/2022]
Abstract
Previous studies were mainly focused on genomic evolution and diversity of type species of Bifidobacterium genus due to their health-promoting effect on host. However, those studies were mainly based on species-level taxonomic resolution, adaptation, and characterization of carbohydrate metabolic features of the bifidobacterial species. Here, a comprehensive analysis of the type strain genome unveils the association of pan-genome evolution with the divergence of metabolic function of the Bifidobacterium genus. This study has also demonstrated that horizontal gene transfer, as well as genome expansion and reduction events, leads to the divergence of metabolic functions in Bifidobacterium genus. Furthermore, the genome-based search of probiotic traits among all the available bifidobacterial type strains gives hints on type species, that could confer health benefits to nutrient-deficient individuals. Altogether, the present study provides insight into the developments of genomic evolution, functional divergence, and potential probiotic type species of the Bifidobacterium genus.
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Affiliation(s)
- Sushanta Deb
- Department of Molecular Biology and Bioinformatics, Tripura University, Suryamaninagar, 799022, Tripura, India. .,All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India.
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García-Santibañez T, Rosenblueth M, Bolaños LM, Martínez-Romero J, Martínez-Romero E. The divergent genome of Scorpion Group 1 (SG1) intracellular bacterium from the venom glands of Vaejovis smithi (Scorpiones: Vaejovidae). Syst Appl Microbiol 2022; 45:126358. [PMID: 36174465 DOI: 10.1016/j.syapm.2022.126358] [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: 05/13/2022] [Revised: 08/12/2022] [Accepted: 09/07/2022] [Indexed: 10/31/2022]
Abstract
Scorpions were among the first animals on land around 430 million years ago. Like many arachnids, scorpions have evolved complex venoms used to paralyze their prey and for self-defense. Here we sequenced and analyzed the metagenomic DNA from venom glands from Vaejovis smithi scorpions. A metagenome-assembled genome (MAG) of 624,025 bp was obtained corresponding to the previously reported Scorpion Group 1 (SG1). The SG1 genome from venom glands had a low GC content (25.8%) characteristic of reduced genomes, many hypothetical genes and genes from the reported minimal set of bacterial genes. Phylogenomic reconstructions placed the uncultured SG1 distant from other reported bacteria constituting a taxonomic novelty. By PCR we detected SG1 in all tested venom glands from 30 independent individuals. Microscopically, we observed SG1 inside epithelial cells from the venom glands using FISH and its presence in scorpion embryos suggested that SG1 is transferred from mother to offspring.
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Affiliation(s)
| | - Mónica Rosenblueth
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis M Bolaños
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico; School of Biosciences, University of Exeter, Exeter, UK
| | - Julio Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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12
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Yang G, Wang Y, Fang Y, An J, Hou X, Lu J, Zhu R, Liu S. A Novel Potent Crystalline Chitin Decomposer: Chitin Deacetylase from Acinetobacter schindleri MCDA01. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165345. [PMID: 36014581 PMCID: PMC9416191 DOI: 10.3390/molecules27165345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022]
Abstract
Chitosan is a functional ingredient that is widely used in food chemistry as an emulsifier, flocculant, antioxidant, or preservative. Chitin deacetylases (CDAs) can catalyze the hydrolysis of acetyl groups, making them useful in the clean production of chitosan. However, the high inactivity of crystalline chitin catalyzed by CDAs has been regarded as the technical bottleneck of crystalline chitin deacetylation. Here, we mined the AsCDA gene from the genome of Acinetobacter schindleri MCDA01 and identified a member of the uraD_N-term-dom superfamily, which was a novel chitin deacetylase with the highest deacetylation activity. The AsCDA gene was expressed in Escherichia coli BL21 by IPTG induction, whose activity to colloidal chitin, α-chitin, and β-chitin reached 478.96 U/mg, 397.07 U/mg, and 133.27 U/mg, respectively. In 12 h, the enzymatic hydrolysis of AsCDA removed 63.05% of the acetyl groups from α-chitin to prepare industrial chitosan with a degree of deacetylation higher than 85%. AsCDA, as a potent chitin decomposer in the production of chitosan, plays a positive role in the upgrading of the chitosan industry and the value-added utilization of chitin biological resources.
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Affiliation(s)
- Guang Yang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang 222000, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yuhan Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yaowei Fang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang 222000, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jia An
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiaoyue Hou
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang 222000, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jing Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang 222000, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Rongjun Zhu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
| | - Shu Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222005, China
- Co-Innovation Center of Jiangsu Marine Bio-Industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
- Jiangsu Marine Resources Development Research Institute, Jiangsu Ocean University, Lianyungang 222000, China
- College of Food Science and Engineering, Jiangsu Ocean University, Lianyungang 222005, China
- Correspondence: ; Tel./Fax: +86-05-15861246008
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13
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dos Santos Ferreira N, Coniglio A, Puente M, Sant’Anna FH, Maroniche G, García J, Molina R, Nievas S, Volpiano CG, Ambrosini A, Passaglia LMP, Pedraza RO, Reis VM, Zilli JÉ, Cassan F. Genome-based reclassification of Azospirillum brasilense Az39 as the type strain of Azospirillum argentinense sp. nov. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain Az39T of
Azospirillum
is a diazotrophic plant growth-promoting bacterium isolated in 1982 from the roots of wheat plants growing in Marcos Juárez, Córdoba, Argentina. It produces indole-3-acetic acid in the presence of l-tryptophan as a precursor, grows at 20–38 °C (optimal 38 °C), and the cells are curved or spiral-shaped, with diameters ranging from 0.5–0.9 to 1.8–2.2 µm. They contain C16 : 0, C18 : 0 and C18 : 1
ω7c/ω6c as the main fatty acids. Phylogenetic analysis of its 16S rRNA gene sequence confirmed that this strain belongs to the genus
Azospirillum
, showing a close relationship with
Azospirillum baldaniorum
Sp245T,
Azospirillum brasilense
Sp7T and
Azospirillum formosense
CC-Nfb-7T. Housekeeping gene analysis revealed that Az39T, together with five strains of the genus (Az19, REC3, BR 11975, MTCC4035 and MTCC4036), form a cluster apart from
A. baldaniorum
Sp245T,
A. brasilense
Sp7T and
A. formosense
CC-Nfb-7T. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) between Az39T and the aforementioned type strains revealed values below 96 %, the circumscription limit for the species delineation (ANI: 95.3, 94.1 and 94.0 %; dDDH: 62.9, 56.3 and 55.6 %). Furthermore, a phylogeny evaluation of the core proteome, including 809 common shared proteins, showed an independent grouping of Az39T, Az19, REC3, BR 11975, MTCC4035 and MTCC4036. The G+C content in the genomic DNA of these six strains varied from 68.3 to 68.5 %. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we consider that strain Az39T, along with strains Az19, REC3, BR 11975, MTCC4035 and MTCC4036, are members of a new
Azospirillum
species, for which the name Azospirillum argentinense sp. nov. is proposed. The type strain is Az39T (=LBPCV39T=BR 148428T=CCCT 22.01T).
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Affiliation(s)
- Natália dos Santos Ferreira
- Programa de Pós-Graduação em Agronomia-Ciência do Solo, Universidade Federal Rural do Rio de Janeiro, BR 465 Km 7, 23890-000 Seropédica, Rio de Janeiro, Brazil
| | - Anahí Coniglio
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
| | - Mariana Puente
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, Nicolás Repetto y de los Reseros, Hurlingham 1686, Buenos Aires, Argentina
| | | | - Guillermo Maroniche
- Facultad de Ciencias Agrarias, CONICET, Universidad Nacional de Mar del Plata, km 73.5, km 73.5, 20 B7620, Buenos Aires, Argentina
| | - Julia García
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Microbiología y Zoología Agrícola, Nicolás Repetto y de los Reseros, Hurlingham 1686, Buenos Aires, Argentina
| | - Romina Molina
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
| | - Sofia Nievas
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
| | - Camila Gazolla Volpiano
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brazil
| | - Adriana Ambrosini
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brazil
| | - Luciane M. P. Passaglia
- Departamento de Genética and Programa de Pós-graduação em Genética e Biologia Molecular, Instituto de Biociências, 9500, Bento Gonçalves Ave, Porto Alegre, RS, Brazil
| | - Raul O. Pedraza
- Facultad de Agronomía y Zootecnia, Universidad Nacional de Tucumán, Av. Kirchner 1900. (4000) 24 San Miguel de Tucumán, Tucumán, Argentina
| | | | - Jerri Édson Zilli
- Embrapa Agrobiologia, BR 465 Km 7, 23891-000, Seropédica, Rio de Janeiro, Brazil
| | - Fabricio Cassan
- Laboratorio de Fisiología Vegetal y de la Interacción Planta-Microorganismo, Instituto de Investigaciones Agrobiotecnológicas (INIAB-CONICET) FCEFQyN, Universidad Nacional de Río Cuarto, Ruta 36, Km 601, Río Cuarto, Ruta 36, Km 601, Río Cuarto, Córdoba, Argentina
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14
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Rivera-Ramírez A, Salgado-Morales R, Jiménez-Pérez A, Pérez-Martínez R, García-Gómez BI, Dantán-González E. Comparative Genomics and Pathogenicity Analysis of Two Bacterial Symbionts of Entomopathogenic Nematodes: The Role of the GroEL Protein in Virulence. Microorganisms 2022; 10:microorganisms10030486. [PMID: 35336062 PMCID: PMC8950339 DOI: 10.3390/microorganisms10030486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 01/27/2023] Open
Abstract
Bacteria of the genera Xenorhabdus and Photorhabdus are symbionts of entomopathogenic nematodes. Despite their close phylogenetic relationship, they show differences in their pathogenicity and virulence mechanisms in target insects. These differences were explored by the analysis of the pangenome, as it provides a framework for characterizing and defining the gene repertoire. We performed the first pangenome analysis of 91 strains of Xenorhabdus and Photorhabdus; the analysis showed that the Photorhabdus genus has a higher number of genes associated with pathogenicity. However, biological tests showed that whole cells of X. nematophila SC 0516 were more virulent than those of P. luminescens HIM3 when both were injected into G. mellonella larvae. In addition, we cloned and expressed the GroEL proteins of both bacteria, as this protein has been previously indicated to show insecticidal activity in the genus Xenorhabdus. Among these proteins, Cpn60-Xn was found to be the most toxic at all concentrations tested, with an LC50 value of 102.34 ng/larva. Sequence analysis suggested that the Cpn60-Xn toxin was homologous to Cpn60-Pl; however, Cpn60-Xn contained thirty-five differentially substituted amino acid residues that could be responsible for its insecticidal activity.
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Affiliation(s)
- Abraham Rivera-Ramírez
- Instituto de Investigaciones en Ciencias Básicas y Aplicadas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, Mexico;
| | - Rosalba Salgado-Morales
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, Mexico; (R.S.-M.); (R.P.-M.)
| | - Alfredo Jiménez-Pérez
- Centro de Desarrollo de Productos Bióticos, Instituto Politécnico Nacional, Calle Ceprobi No. 8, San Isidro, Yautepec 62739, Morelos, Mexico;
| | - Rebeca Pérez-Martínez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, Mexico; (R.S.-M.); (R.P.-M.)
| | - Blanca Inés García-Gómez
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Apdo. Postal 510-3, Cuernavaca 62250, Morelos, Mexico;
| | - Edgar Dantán-González
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Chamilpa, Cuernavaca 62209, Morelos, Mexico; (R.S.-M.); (R.P.-M.)
- Correspondence: ; Tel.: +52-777-329-7000
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15
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Contreras-Moreira B, Del Río ÁR, Cantalapiedra CP, Sancho R, Vinuesa P. Pangenome Analysis of Plant Transcripts and Coding Sequences. Methods Mol Biol 2022; 2512:121-152. [PMID: 35818004 DOI: 10.1007/978-1-0716-2429-6_9] [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: 06/15/2023]
Abstract
The pangenome of a species is the sum of the genomes of its individuals. As coding sequences often represent only a small fraction of each genome, analyzing the pangene set can be a cost-effective strategy for plants with large genomes or highly heterozygous species. Here, we describe a step-by-step protocol to analyze plant pangene sets with the software GET_HOMOLOGUES-EST . After a short introduction, where the main concepts are illustrated, the remaining sections cover the installation and typical operations required to analyze and annotate pantranscriptomes and gene sets of plants. The recipes include instructions on how to call core and accessory genes, how to compute a presence-absence pangenome matrix, and how to identify and analyze private genes, present only in some genotypes. Downstream phylogenetic analyses are also discussed.
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Affiliation(s)
| | | | | | - Rubén Sancho
- Estación Experimental de Aula Dei-CSIC, Zaragoza, Spain
- Escuela Politécnica Superior, Universidad de Zaragoza, Huesca, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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16
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Abstract
Animal tuberculosis (TB) is an emergent disease caused by Mycobacterium bovis, one of the animal-adapted ecotypes of the Mycobacterium tuberculosis complex (MTC). In this work, whole-genome comparative analyses of 70 M. bovis were performed to gain insights into the pan-genome architecture. The comparison across M. bovis predicted genome composition enabled clustering into the core- and accessory-genome components, with 2736 CDS for the former, while the accessory moiety included 3897 CDS, of which 2656 are restricted to one/two genomes only. These analyses predicted an open pan-genome architecture, with an average of 32 CDS added by each genome and show the diversification of discrete M. bovis subpopulations supported by both core- and accessory-genome components. The functional annotation of the pan-genome classified each CDS into one or several COG (Clusters of Orthologous Groups) categories, revealing ‘transcription’ (total average CDSs, n=258), ‘lipid metabolism and transport’ (n=242), ‘energy production and conversion’ (n=214) and ‘unknown function’ (n=876) as the most represented. The closer analysis of polymorphisms in virulence-related genes in a restrict group of M. bovis from a multi-host system enabled the identification of clade-monomorphic non-synonymous SNPs, illustrating clade-specific virulence landscapes and correlating with disease severity. This first comparative pan-genome study of a diverse collection of M. bovis encompassing all clonal complexes indicates a high percentage of accessory genes and denotes an open, dynamic non-conservative pan-genome structure, with high evolutionary potential, defying the canons of MTC biology. Furthermore, it shows that M. bovis can shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion, adaptation and persistence.
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Affiliation(s)
- Ana C Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.,Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.,Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
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17
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Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP. Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. mSystems 2021; 6:e0042521. [PMID: 34546072 PMCID: PMC8547433 DOI: 10.1128/msystems.00425-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.
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Affiliation(s)
| | - Silvio D. Brugger
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Isabel Fernandez Escapa
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | | | - Sean L. Cotton
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Sara M. Eslami
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Lindsey Bomar
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | - Tommy H. Tran
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Dakota S. Jones
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Samuel Minot
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Christopher D. Johnston
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, Boston, Massachusetts, USA
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Katherine P. Lemon
- The Forsyth Institute (Microbiology), Cambridge, Massachusetts, USA
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Section of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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18
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Starwalt-Lee R, El-Naggar MY, Bond DR, Gralnick JA. Electrolocation? The evidence for redox-mediated taxis in Shewanella oneidensis. Mol Microbiol 2020; 115:1069-1079. [PMID: 33200455 DOI: 10.1111/mmi.14647] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/11/2020] [Indexed: 11/27/2022]
Abstract
Shewanella oneidensis is a dissimilatory metal reducing bacterium and model for extracellular electron transfer (EET), a respiratory mechanism in which electrons are transferred out of the cell. In the last 10 years, migration to insoluble electron acceptors for EET has been shown to be nonrandom and tactic, seemingly in the absence of molecular or energy gradients that typically allow for taxis. As the ability to sense, locate, and respire electrodes has applications in bioelectrochemical technology, a better understanding of taxis in S. oneidensis is needed. While the EET conduits of S. oneidensis have been studied extensively, its taxis pathways and their interplay with EET are not yet understood, making investigation into taxis phenomena nontrivial. Since S. oneidensis is a member of an EET-encoding clade, the genetic circuitry of taxis to insoluble acceptors may be conserved. We performed a bioinformatic analysis of Shewanella genomes to identify S. oneidensis chemotaxis orthologs conserved in the genus. In addition to the previously reported core chemotaxis gene cluster, we identify several other conserved proteins in the taxis signaling pathway. We present the current evidence for the two proposed models of EET taxis, "electrokinesis" and flavin-mediated taxis, and highlight key areas in need of further investigation.
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Affiliation(s)
- Ruth Starwalt-Lee
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA.,Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Daniel R Bond
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota - Twin Cities, St. Paul, MN, USA
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19
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Ghaly TM, Paulsen IT, Sajjad A, Tetu SG, Gillings MR. A Novel Family of Acinetobacter Mega-Plasmids Are Disseminating Multi-Drug Resistance Across the Globe While Acquiring Location-Specific Accessory Genes. Front Microbiol 2020; 11:605952. [PMID: 33343549 PMCID: PMC7738440 DOI: 10.3389/fmicb.2020.605952] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/10/2020] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter species are emerging as major nosocomial pathogens, aided by their ability to acquire resistance to all classes of antibiotics. A key factor leading to their multi-drug resistance phenotypes is the acquisition of a wide variety of mobile genetic elements, particularly large conjugative plasmids. Here, we characterize a family of 21 multi-drug resistance mega-plasmids in 11 different Acinetobacter species isolated from various locations across the globe. The plasmid family exhibits a highly dynamic and diverse accessory genome, including 221 antibiotic resistance genes (ARGs) that confer resistance to 13 classes of antibiotics. We show that plasmids isolated within the same geographic region are often evolutionarily divergent members of this family based on their core-genome, yet they exhibit a more similar accessory genome. Individual plasmids, therefore, can disseminate to different locations around the globe, where they then appear to acquire diverse sets of accessory genes from their local surroundings. Further, we show that plasmids from several geographic regions were enriched with location-specific functional traits. Together, our findings show that these mega-plasmids can transmit across species boundaries, have the capacity for global dissemination, can accumulate a diverse suite of location-specific accessory genes, and can confer multi-drug resistance phenotypes of significant concern for human health. We therefore highlight this previously undescribed plasmid family as a serious threat to healthcare systems worldwide. These findings also add to the growing concern that mega-plasmids are key disseminators of antibiotic resistance and require global surveillance.
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Affiliation(s)
- Timothy M. Ghaly
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ian T. Paulsen
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Ammara Sajjad
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
| | - Sasha G. Tetu
- Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
| | - Michael R. Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW, Australia
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20
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Österholm J, Popin RV, Fewer DP, Sivonen K. Phylogenomic Analysis of Secondary Metabolism in the Toxic Cyanobacterial Genera Anabaena, Dolichospermum and Aphanizomenon. Toxins (Basel) 2020; 12:E248. [PMID: 32290496 PMCID: PMC7232259 DOI: 10.3390/toxins12040248] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 04/08/2020] [Accepted: 04/09/2020] [Indexed: 01/20/2023] Open
Abstract
Cyanobacteria produce an array of toxins that pose serious health risks to humans and animals. The closely related diazotrophic genera, Anabaena, Dolichospermum, and Aphanizomenon, frequently form poisonous blooms in lakes and brackish waters around the world. These genera form a complex now termed the Anabaena, Dolichospermum, and Aphanizomenon (ADA) clade and produce a greater array of toxins than any other cyanobacteria group. However, taxonomic confusion masks the distribution of toxin biosynthetic pathways in cyanobacteria. Here we obtained 11 new draft genomes to improve the understanding of toxin production in these genera. Comparison of secondary metabolite pathways in all available 31 genomes for these three genera suggests that the ability to produce microcystin, anatoxin-a, and saxitoxin is associated with specific subgroups. Each toxin gene cluster was concentrated or even limited to a certain subgroup within the ADA clade. Our results indicate that members of the ADA clade encode a variety of secondary metabolites following the phylogenetic clustering of constituent species. The newly sequenced members of the ADA clade show that phylogenetic separation of planktonic Dolichospermum and benthic Anabaena is not complete. This underscores the importance of taxonomic revision of Anabaena, Dolichospermum, and Aphanizomenon genera to reflect current phylogenomic understanding.
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Affiliation(s)
| | | | | | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland; (J.Ö.); (R.V.P.); (D.P.F.)
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21
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Popin RV, Delbaje E, de Abreu VAC, Rigonato J, Dörr FA, Pinto E, Sivonen K, Fiore MF. Genomic and Metabolomic Analyses of Natural Products in Nodularia spumigena Isolated from a Shrimp Culture Pond. Toxins (Basel) 2020; 12:toxins12030141. [PMID: 32106513 PMCID: PMC7150779 DOI: 10.3390/toxins12030141] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/13/2020] [Accepted: 02/21/2020] [Indexed: 11/16/2022] Open
Abstract
The bloom-forming cyanobacterium Nodularia spumigena CENA596 encodes the biosynthetic gene clusters (BGCs) of the known natural products nodularins, spumigins, anabaenopeptins/namalides, aeruginosins, mycosporin-like amino acids, and scytonemin, along with the terpenoid geosmin. Targeted metabolomics confirmed the production of these metabolic compounds, except for the alkaloid scytonemin. Genome mining of N. spumigena CENA596 and its three closely related Nodularia strains—two planktonic strains from the Baltic Sea and one benthic strain from Japanese marine sediment—revealed that the number of BGCs in planktonic strains was higher than in benthic one. Geosmin—a volatile compound with unpleasant taste and odor—was unique to the Brazilian strain CENA596. Automatic annotation of the genomes using subsystems technology revealed a related number of coding sequences and functional roles. Orthologs from the Nodularia genomes are involved in the primary and secondary metabolisms. Phylogenomic analysis of N. spumigena CENA596 based on 120 conserved protein sequences positioned this strain close to the Baltic Nodularia. Phylogeny of the 16S rRNA genes separated the Brazilian CENA596 strain from those of the Baltic Sea, despite their high sequence identities (99% identity, 100% coverage). The comparative analysis among planktic Nodularia strains showed that their genomes were considerably similar despite their geographically distant origin.
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Affiliation(s)
- Rafael Vicentini Popin
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Endrews Delbaje
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Vinicius Augusto Carvalho de Abreu
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Institute of Exact and Natural Sciences, Federal University of Pará, Rua Augusto Corrêa 1, Belém 66075-10, Pará, Brazil
| | - Janaina Rigonato
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
| | - Felipe Augusto Dörr
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Ernani Pinto
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Faculty of Pharmaceutical Sciences, University of São Paulo, Avenida Professor Lineu Prestes, São Paulo 05508-000, São Paulo, Brazil;
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland;
| | - Marli Fatima Fiore
- Center for Nuclear Energy in Agriculture, University of São Paulo, Avenida Centenário 303, Piracicaba 13400-970, São Paulo, Brazil; (R.V.P.); (E.D.); (V.A.C.d.A.); (J.R.); (E.P.)
- Correspondence:
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22
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Gostinčar C, Turk M, Zajc J, Gunde‐Cimerman N. Fifty Aureobasidium pullulans genomes reveal a recombining polyextremotolerant generalist. Environ Microbiol 2019; 21:3638-3652. [PMID: 31112354 PMCID: PMC6852026 DOI: 10.1111/1462-2920.14693] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/17/2019] [Accepted: 05/20/2019] [Indexed: 01/31/2023]
Abstract
The black yeast Aureobasidium pullulans is a textbook example of a generalistic and ubiquitous fungus thriving in a wide variety of environments. To investigate whether A. pullulans is a true generalist, or alternatively, whether part of its versatility can be attributed to intraspecific specialization masked by cryptic diversification undetectable by traditional phylogenetic analyses, we sequenced and analysed the genomes of 50 strains of A. pullulans from different habitats and geographic locations. No population structure was observed in the sequenced strains. Decay of linkage disequilibrium over shorter physical distances (<100 bp) than in many sexually reproducing fungi indicates a high level of recombination in the species. A homothallic mating locus was found in all of the sequenced genomes. Aureobasidium pullulans appears to have a homogeneous population genetics structure, which is best explained by good dispersal and high levels of recombination. This means that A. pullulans is a true generalist that can inhabit different habitats without substantial specialization to any of these habitats at the genomic level. Furthermore, in the future, the high level of A. pullulans recombination can be exploited for the identification of genomic loci that are involved in the many biotechnologically useful traits of this black yeast.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
- Lars Bolund Institute of Regenerative Medicine, BGI‐QingdaoQingdao 266555China
| | - Martina Turk
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
| | - Janja Zajc
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
- National Institute of BiologyVečna pot 111, SI‐1000LjubljanaSlovenia
| | - Nina Gunde‐Cimerman
- Department of Biology, Biotechnical FacultyUniversity of Ljubljana, Jamnikarjeva 101, SI‐1000LjubljanaSlovenia
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23
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Gostinčar C, Sun X, Zajc J, Fang C, Hou Y, Luo Y, Gunde-Cimerman N, Song Z. Population Genomics of an Obligately Halophilic Basidiomycete Wallemia ichthyophaga. Front Microbiol 2019; 10:2019. [PMID: 31551960 PMCID: PMC6738226 DOI: 10.3389/fmicb.2019.02019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/19/2019] [Indexed: 11/15/2022] Open
Abstract
Background Wallemia ichthyophaga is a highly specialized basidiomycetous fungus. It is one of the most halophilic fungi ever described, only able to grow at low water activity. This specialization is thought to explain why it is only rarely isolated from nature. Results Genomes of 21 W. ichthyophaga strains were sequenced with PE150 reads on BGISEQ500 platform. The genomes shared high similarity with the reference genome of the species, they were all smaller than 10 Mbp and had a low number of predicted genes. Groups of strains isolated in the same location encompassed clones as well as very divergent strains. There was little concordance between phylogenies of predicted genes. Linkage disequilibrium of pairs of polymorphic loci decayed relatively quickly as a function of distance between the loci (LD decay distance 1270 bp). For the first time a putative mating-type locus was identified in the genomes of W. ichthyophaga. Conclusion Based on the comparison of W. ichthyophaga genomes it appears that some phylogenetic lineages of the species can persist in the same location over at least several years. Apart from this, the differences between the strains do not reflect the isolation habitat or geographic location. Together with results supporting the existence of (sexual) recombination in W. ichthyophaga, the presented results indicate that strains of W. ichthyophaga can form a single recombining population even between different habitats and over large geographical distances.
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Affiliation(s)
- Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China
| | - Xiaohuan Sun
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Janja Zajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,National Institute of Biology, Ljubljana, Slovenia
| | - Chao Fang
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yong Hou
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Yonglun Luo
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Zewei Song
- BGI-Shenzhen, Shenzhen, China.,China National GeneBank, BGI-Shenzhen, Shenzhen, China
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24
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Paniagua-Contreras GL, Monroy-Pérez E, Díaz-Velásquez CE, Uribe-García A, Labastida A, Peñaloza-Figueroa F, Domínguez-Trejo P, García LR, Vaca-Paniagua F, Vaca S. Whole-genome sequence analysis of multidrug-resistant uropathogenic strains of Escherichia coli from Mexico. Infect Drug Resist 2019; 12:2363-2377. [PMID: 31447566 PMCID: PMC6682767 DOI: 10.2147/idr.s203661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 06/17/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Escherichia coli is the main bacterium associated with urinary tract infections (UTIs), including cystitis and pyelonephritis. Uropathogenic E. coli (UPEC) harbors numerous genes that encode diverse virulence factors contributing to its pathogenicity. The treatment of UTIs has become complicated due to the natural selection of E. coli strains that are multiresistant to several groups of antibiotics regularly used in clinical settings such as hospitals. Genomic reports of the global composition and distribution of the antibiotic resistance and virulence genes of these pathogenic strains are lacking in the Mexican population. Purpose and methods: The aim of this study was to globally characterize the genomes of a group of UPEC strains by massive parallel sequencing to determine the prevalence and distribution of virulence and antibiotic resistance genes associated with different serotypes and phylogenetic groups. Results: The strains exhibited 138-197 virulence genes and 29 antibiotic resistance genes related to antibiotics that are commonly used in clinical practice. Conclusions: These findings are relevant to the definition of new strategies for treating urinary tract infections in public hospitals and private practice. To further define the epidemiological distribution and composition of these virulence and antibiotic resistance genes, larger studies are needed.
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Affiliation(s)
- G L Paniagua-Contreras
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, México
| | - E Monroy-Pérez
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, México
| | - C E Díaz-Velásquez
- Laboratorio Nacional en Salud: Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-
Degenerativas, FES-Iztacala, UNAM, Tlalnepantla, Edo. de México, México
| | - A Uribe-García
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, México
| | | | | | | | - L R García
- Instituto Mexicano del Seguro Social , México City, México
| | - F Vaca-Paniagua
- Laboratorio Nacional en Salud: Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-
Degenerativas, FES-Iztacala, UNAM, Tlalnepantla, Edo. de México, México.,Subdirección de Investigación Básica, Instituto Nacional de Cancerología, México City, México.,Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, México
| | - S Vaca
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla, México
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25
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Thanki AM, Brown N, Millard AD, Clokie MRJ. Genomic Characterization of Jumbo Salmonella Phages That Effectively Target United Kingdom Pig-Associated Salmonella Serotypes. Front Microbiol 2019; 10:1491. [PMID: 31312191 PMCID: PMC6614189 DOI: 10.3389/fmicb.2019.01491] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/14/2019] [Indexed: 12/13/2022] Open
Abstract
A common cause of human food poisoning is through ingestion of pork products contaminated with Salmonella spp. Worryingly multi-drug resistant (MDR) Salmonella strains have been isolated from pigs, which motivates the need for alternative antimicrobials. In this study isolation and characterization of 21 lytic Salmonella phages is described. All 21 phages, labeled as SPFM phages were shown to efficiently infect MDR Salmonella strains isolated from United Kingdom pigs and phages SPFM1, SPFM3, SPFM10, SPFM14, SPFM15, SPFM17, and SPFM19 could lyse 100% of strains tested. The phage genome sizes range from 233 to 242 Kb, which qualifies them as jumbo phages. All SPFM phage genomes are approximately 95% similar to each other by average nucleotide identity, they encode between 258-307 coding sequences and share 188 core genes. Phylogenetic analysis shows these phages are most similar to phages of the genus Seoulvirus and to further characterize phages within the genus, genes under positive selection were identified. Several of the genes under evolutionary selection pressure were predicted to encode for proteins that interact with bacteria. We describe the phenotypic and genetic characterization of this novel Salmonella phage set. As the phages efficiently kill MDR Salmonella strains, they may offer a promising alternative to antibiotics.
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Affiliation(s)
| | | | | | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
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26
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Sun X, Gostinčar C, Fang C, Zajc J, Hou Y, Song Z, Gunde-Cimerman N. Genomic Evidence of Recombination in the Basidiomycete Wallemia mellicola. Genes (Basel) 2019; 10:genes10060427. [PMID: 31167502 PMCID: PMC6628117 DOI: 10.3390/genes10060427] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/16/2022] Open
Abstract
One of the most commonly encountered species in the small basidiomycetous sub-phylum Wallemiomycotina is Wallemia mellicola, a xerotolerant fungus with a widespread distribution. To investigate the population characteristics of the species, whole genomes of twenty-five strains were sequenced. Apart from identification of four strains of clonal origin, the distances between the genomes failed to reflect either the isolation habitat of the strains or their geographical origin. Strains from different parts of the world appeared to represent a relatively homogenous and widespread population. The lack of concordance between individual gene phylogenies and the decay of linkage disequilibrium indicated that W. mellicola is at least occasionally recombining. Two versions of a putative mating-type locus have been found in all sequenced genomes, each present in approximately half of the strains. W. mellicola thus appears to be capable of (sexual) recombination and shows no signs of allopatric speciation or specialization to specific habitats.
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Affiliation(s)
- Xiaohuan Sun
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Cene Gostinčar
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China.
| | - Chao Fang
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Janja Zajc
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
- Department of Biotechnology and Systems biology, National Institute of Biology, 1000 Ljubljana, Slovenia.
| | - Yong Hou
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Zewei Song
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China.
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen 518083, China.
| | - Nina Gunde-Cimerman
- Department of Biology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia.
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27
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Teikari JE, Popin RV, Hou S, Wahlsten M, Hess WR, Sivonen K. Insight into the genome and brackish water adaptation strategies of toxic and bloom-forming Baltic Sea Dolichospermum sp. UHCC 0315. Sci Rep 2019; 9:4888. [PMID: 30894564 PMCID: PMC6426976 DOI: 10.1038/s41598-019-40883-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/22/2019] [Indexed: 11/09/2022] Open
Abstract
The Baltic Sea is a shallow basin of brackish water in which the spatial salinity gradient is one of the most important factors contributing to species distribution. The Baltic Sea is infamous for its annual cyanobacterial blooms comprised of Nodularia spumigena, Aphanizomenon spp., and Dolichospermum spp. that cause harm, especially for recreational users. To broaden our knowledge of the cyanobacterial adaptation strategies for brackish water environments, we sequenced the entire genome of Dolichospermum sp. UHCC 0315, a species occurring not only in freshwater environments but also in brackish water. Comparative genomics analyses revealed a close association with Dolichospermum sp. UHCC 0090 isolated from a lake in Finland. The genome closure of Dolichospermum sp. UHCC 0315 unraveled a mixture of two subtypes in the original culture, and subtypes exhibited distinct buoyancy phenotypes. Salinity less than 3 g L-1 NaCl enabled proper growth of Dolichospermum sp. UHCC 0315, whereas growth was arrested at moderate salinity (6 g L-1 NaCl). The concentrations of toxins, microcystins, increased at moderate salinity, whereas RNA sequencing data implied that Dolichospermum remodeled its primary metabolism in unfavorable high salinity. Based on our results, the predicted salinity decrease in the Baltic Sea may favor toxic blooms of Dolichospermum spp.
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Affiliation(s)
- Jonna E Teikari
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Rafael V Popin
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Shengwei Hou
- Genetics & Experimental Bioinformatics, Institute of Biology III, University Freiburg, Schänzlestraße 1, D-79104, Freiburg, Germany
| | - Matti Wahlsten
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Wolfgang R Hess
- Genetics & Experimental Bioinformatics, Institute of Biology III, University Freiburg, Schänzlestraße 1, D-79104, Freiburg, Germany
| | - Kaarina Sivonen
- Department of Microbiology, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland.
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28
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Giner-Lamia J, Vinuesa P, Betancor L, Silva C, Bisio J, Soleto L, Chabalgoity JA, Puente JL, García-del Portillo F. Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256. BMC Genomics 2019; 20:99. [PMID: 30704413 PMCID: PMC6357384 DOI: 10.1186/s12864-018-5352-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasive human infections. The factors contributing to this unusual behavior are currently unknown. RESULTS We report here the genome features of two diarizonae strains, SBO13 and SBO27, isolated from endocervical tissue collected post-abortion and from cerebrospinal fluid of a newborn child, respectively, in the city of Santa Cruz, Bolivia. Although isolated six years apart, SBO27 in 2008 and SBO13 in 2014, both strains belong to the same sequence type 1256 (ST1256) and show a high degree of genome conservation sharing more than 99% of their genes, including the conservation of a ~ 10 kb plasmid. A prominent feature of the two genomes is the presence of 24 genomic islands (GIs), in addition to 10 complete Salmonella pathogenicity islands (SPI) and fragments of SPI-7, a pathogenicity island first reported in the human-adapted serovar Typhi. Some of the GIs identified in SBO13 and SBO27 harbor genes putatively encoding auto-transporters involved in adhesion, lipopolysaccharide modifying enzymes, putative toxins, pili-related proteins, efflux pumps, and several putative membrane cation transport related-genes, among others. These two Bolivian isolates also share genes encoding the type-III secretion system effector proteins SseK2, SseK3 and SlrP with other diarizonae sequence types (ST) mainly-associated with infections in humans. The sseK2, sseK3 and slrP genes were either absent or showing frameshift mutations in a significant proportion of genomes from environmental diarizonae isolates. CONCLUSIONS The comparative genomic study of two diarizonae strains isolated in Bolivia from human patients uncovered the presence of many genes putatively related to virulence. The statistically-significant acquisition of a unique combination of these functions by diarizonae strains isolated from humans may have impacted the ability of these isolates to successfully infect the human host.
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Affiliation(s)
- Joaquín Giner-Lamia
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Claudia Silva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Julieta Bisio
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Lorena Soleto
- Ministerio de Salud de Bolivia, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz, Bolivia
- Universidad Autónoma Gabriel René Moreno, Santa Cruz, Bolivia
| | - José A. Chabalgoity
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - José Luis Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Francisco García-del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
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29
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Delaye L, Ruiz-Ruiz S, Calderon E, Tarazona S, Conesa A, Moya A. Evidence of the Red-Queen Hypothesis from Accelerated Rates of Evolution of Genes Involved in Biotic Interactions in Pneumocystis. Genome Biol Evol 2018; 10:1596-1606. [PMID: 29893833 PMCID: PMC6012782 DOI: 10.1093/gbe/evy116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2018] [Indexed: 01/15/2023] Open
Abstract
Pneumocystis species are ascomycete fungi adapted to live inside the lungs of mammals. These ascomycetes show extensive stenoxenism, meaning that each species of Pneumocystis infects a single species of host. Here, we study the effect exerted by natural selection on gene evolution in the genomes of three Pneumocystis species. We show that genes involved in host interaction evolve under positive selection. In the first place, we found strong evidence of episodic diversifying selection in Major surface glycoproteins (Msg). These proteins are located on the surface of Pneumocystis and are used for host attachment and probably for immune system evasion. Consistent with their function as antigens, most sites under diversifying selection in Msg code for residues with large relative surface accessibility areas. We also found evidence of positive selection in part of the cell machinery used to export Msg to the cell surface. Specifically, we found that genes participating in glycosylphosphatidylinositol (GPI) biosynthesis show an increased rate of nonsynonymous substitutions (dN) versus synonymous substitutions (dS). GPI is a molecule synthesized in the endoplasmic reticulum that is used to anchor proteins to membranes. We interpret the aforementioned findings as evidence of selective pressure exerted by the host immune system on Pneumocystis species, shaping the evolution of Msg and several proteins involved in GPI biosynthesis. We suggest that genome evolution in Pneumocystis is well described by the Red-Queen hypothesis whereby genes relevant for biotic interactions show accelerated rates of evolution.
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Affiliation(s)
- Luis Delaye
- Departamento de Ingeniería Genética, CINVESTAV Irapuato, Guanajuato, México
| | - Susana Ruiz-Ruiz
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain
| | - Enrique Calderon
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/Consejo Superior de Investigaciones Científicas/Universidad de Sevilla.,Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Sonia Tarazona
- Centro de Investigacion Principe Felipe, València, Spain.,Departamento de Estadística e Investigación Operativa Aplicadas y Calidad, Universitat Politècnica de València, Spain
| | - Ana Conesa
- Centro de Investigacion Principe Felipe, València, Spain.,Microbiology and Cell Science, University of Florida
| | - Andrés Moya
- Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana (FISABIO)-Salud Pública, València, Spain.,Institute for Integrative Systems Biology, Universitat de València, Spain
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30
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Sandner-Miranda L, Vinuesa P, Cravioto A, Morales-Espinosa R. The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the Genus Serratia. Front Microbiol 2018; 9:828. [PMID: 29867787 PMCID: PMC5958200 DOI: 10.3389/fmicb.2018.00828] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/11/2018] [Indexed: 12/18/2022] Open
Abstract
Serratia marcescens, a member of the Enterobacteriaceae family, was long thought to be a non-pathogenic bacterium prevalent in environmental habitats. Together with other members of this genus, it has emerged in recent years as an opportunistic nosocomial pathogen causing various types of infections. One important feature of pathogens belonging to this genus is their intrinsic and acquired resistance to a variety of antibiotic families, including β-lactam, aminoglycosides, quinolones and polypeptide antibiotics. The aim of this study was to elucidate which genes participate in the intrinsic and acquired antibiotic resistance of this genus in order to determine the Serratia genus resistome. We performed phylogenomic and comparative genomic analyses using 32 Serratia spp. genomes deposited in the NCBI GenBank from strains isolated from different ecological niches and different lifestyles. S. marcescens strain SmUNAM836, which was previously isolated from a Mexican adult with obstructive pulmonary disease, was included in this study. The results show that most of the antibiotic resistance genes (ARGs) were found on the chromosome, and to a lesser degree, on plasmids and transposons acquired through horizontal gene transfer. Four strains contained the gyrA point mutation in codon Ser83 that confers quinolone resistance. Pathogenic and environmental isolates presented a high number of ARGs, especially genes associated with efflux systems. Pathogenic strains, specifically nosocomial strains, presented more acquired resistance genes than environmental isolates. We may conclude that the environment provides a natural reservoir for antibiotic resistance, which has been underestimated in the medical field.
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Affiliation(s)
- Luisa Sandner-Miranda
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alejandro Cravioto
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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31
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Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas. Front Microbiol 2018; 9:771. [PMID: 29765358 PMCID: PMC5938378 DOI: 10.3389/fmicb.2018.00771] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022] Open
Abstract
The massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM. We demonstrate the practical utility of the software by analyzing 170 Stenotrophomonas genome sequences available in RefSeq and 10 new complete genomes of Mexican environmental S. maltophilia complex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity (cgANIb) of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 16 misclassified RefSeq genome sequences, 14 of them labeled as S. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license at https://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available at https://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.
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Affiliation(s)
- Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luz E Ochoa-Sánchez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas, Zaragoza, Spain.,Fundación Agencia Aragonesa para la Investigacion y el Desarrollo (ARAID), Zaragoza, Spain
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32
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Arriola MB, Velmurugan N, Zhang Y, Plunkett MH, Hondzo H, Barney BM. Genome sequences of Chlorella sorokiniana UTEX 1602 and Micractinium conductrix SAG 241.80: implications to maltose excretion by a green alga. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:566-586. [PMID: 29178410 DOI: 10.1111/tpj.13789] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 11/14/2017] [Indexed: 06/07/2023]
Abstract
Green algae represent a key segment of the global species capable of photoautotrophic-driven biological carbon fixation. Algae partition fixed-carbon into chemical compounds required for biomass, while diverting excess carbon into internal storage compounds such as starch and lipids or, in certain cases, into targeted extracellular compounds. Two green algae were selected to probe for critical components associated with sugar production and release in a model alga. Chlorella sorokiniana UTEX 1602 - which does not release significant quantities of sugars to the extracellular space - was selected as a control to compare with the maltose-releasing Micractinium conductrix SAG 241.80 - which was originally isolated from an endosymbiotic association with the ciliate Paramecium bursaria. Both strains were subjected to three sequencing approaches to assemble their genomes and annotate their genes. This analysis was further complemented with transcriptional studies during maltose release by M. conductrix SAG 241.80 versus conditions where sugar release is minimal. The annotation revealed that both strains contain homologs for the key components of a putative pathway leading to cytosolic maltose accumulation, while transcriptional studies found few changes in mRNA levels for the genes associated with these established intracellular sugar pathways. A further analysis of potential sugar transporters found multiple homologs for SWEETs and tonoplast sugar transporters. The analysis of transcriptional differences revealed a lesser and more measured global response for M. conductrix SAG 241.80 versus C. sorokiniana UTEX 1602 during conditions resulting in sugar release, providing a catalog of genes that might play a role in extracellular sugar transport.
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Affiliation(s)
- Matthew B Arriola
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Natarajan Velmurugan
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Ying Zhang
- Minnesota Supercomputing Institute, University of Minnesota, St. Paul, MN, 55108, USA
| | - Mary H Plunkett
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Hanna Hondzo
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
| | - Brett M Barney
- Biotechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St. Paul, MN, 55108, USA
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33
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Meyer KA, Davis TW, Watson SB, Denef VJ, Berry MA, Dick GJ. Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms. PLoS One 2017; 12:e0183859. [PMID: 29020009 PMCID: PMC5647855 DOI: 10.1371/journal.pone.0183859] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 08/11/2017] [Indexed: 12/15/2022] Open
Abstract
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M. wesenbergii LE013-01) and one from upstream Lake St. Clair (M. cf aeruginosa LSC13-02), and compared these data to the genomes of seventeen Microcystis spp. from across the globe as well as one metagenome and seven metatranscriptomes from a 2014 Lake Erie Microcystis bloom. For the publically available strains analyzed, the core genome is ~1900 genes, representing ~11% of total genes in the pan-genome and ~45% of each strain's genome. The flexible genome content was related to Microcystis subclades defined by phylogenetic analysis of both housekeeping genes and total core genes. To our knowledge this is the first evidence that the flexible genome is linked to the core genome of the Microcystis species complex. The majority of strain-specific genes were present and expressed in bloom communities in Lake Erie. Roughly 8% of these genes from the lower Great Lakes are involved in genome plasticity (rapid gain, loss, or rearrangement of genes) and resistance to foreign genetic elements (such as CRISPR-Cas systems). Intriguingly, strain-specific genes from Microcystis cultured from around the world were also present and expressed in the Lake Erie blooms, suggesting that the Microcystis pangenome is truly global. The presence and expression of flexible genes, including strain-specific genes, suggests that strain-level genomic diversity may be important in maintaining Microcystis abundance during bloom events.
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Affiliation(s)
- Kevin Anthony Meyer
- Cooperative Institute for Great Lakes Research (CIGLR), University of
Michigan, Ann Arbor, MI, United States of America
- Department of Earth and Environmental Sciences, University of Michigan,
Ann Arbor, MI, United States of America
| | - Timothy W. Davis
- NOAA Great Lakes Environmental Research Laboratory, Ann Arbor, MI, United
States of America
| | - Susan B. Watson
- Environment and Climate Change Canada, Burlington, ON,
Canada
| | - Vincent J. Denef
- Department of Ecology and Evolutionary Biology, University of Michigan,
Ann Arbor, MI, United States of America
| | - Michelle A. Berry
- Department of Ecology and Evolutionary Biology, University of Michigan,
Ann Arbor, MI, United States of America
| | - Gregory J. Dick
- Department of Earth and Environmental Sciences, University of Michigan,
Ann Arbor, MI, United States of America
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34
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Abstract
The field of comparative genomics is concerned with the study of similarities and differences between the information encoded in the genomes of organisms. A common approach is to define gene families by clustering protein sequences based on sequence similarity, and analyze protein cluster presence and absence in different species groups as a guide to biology. Due to the high dimensionality of these data, downstream analysis of protein clusters inferred from large numbers of species, or species with many genes, is nontrivial, and few solutions exist for transparent, reproducible, and customizable analyses. We present KinFin, a streamlined software solution capable of integrating data from common file formats and delivering aggregative annotation of protein clusters. KinFin delivers analyses based on systematic taxonomy of the species analyzed, or on user-defined, groupings of taxa, for example, sets based on attributes such as life history traits, organismal phenotypes, or competing phylogenetic hypotheses. Results are reported through graphical and detailed text output files. We illustrate the utility of the KinFin pipeline by addressing questions regarding the biology of filarial nematodes, which include parasites of veterinary and medical importance. We resolve the phylogenetic relationships between the species and explore functional annotation of proteins in clusters in key lineages and between custom taxon sets, identifying gene families of interest. KinFin can easily be integrated into existing comparative genomic workflows, and promotes transparent and reproducible analysis of clustered protein data.
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35
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Karlsen C, Hjerde E, Klemetsen T, Willassen NP. Pan genome and CRISPR analyses of the bacterial fish pathogen Moritella viscosa. BMC Genomics 2017; 18:313. [PMID: 28427330 PMCID: PMC5399434 DOI: 10.1186/s12864-017-3693-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/06/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Winter-ulcer Moritella viscosa infections continue to be a significant burden in Atlantic salmon (Salmo salar L.) farming. M. viscosa comprises two main clusters that differ in genetic variation and phenotypes including virulence. Horizontal gene transfer through acquisition and loss of mobile genetic elements (MGEs) is a major driving force of bacterial diversification. To gain insight into genomic traits that could affect sublineage evolution within this bacterium we examined the genome sequences of twelve M. viscosa strains. Matches between M. viscosa clustered, regularly interspaced, short palindromic, repeats and associated cas genes (CRISPR-Cas) were analysed to correlate CRISPR-Cas with adaptive immunity against MGEs. RESULTS The comparative genomic analysis of M. viscosa isolates from across the North Atlantic region and from different fish species support delineation of M. viscosa into four phylogenetic lineages. The results showed that M. viscosa carries two distinct variants of the CRISPR-Cas subtype I-F systems and that CRISPR features follow the phylogenetic lineages. A subset of the spacer content match prophage and plasmid genes dispersed among the M. viscosa strains. Further analysis revealed that prophage and plasmid-like element distribution were reflected in the content of the CRISPR-spacer profiles. CONCLUSIONS Our data suggests that CRISPR-Cas mediated interactions with MGEs impact genome properties among M. viscosa, and that patterns in spacer and MGE distributions are linked to strain relationships.
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Affiliation(s)
- Christian Karlsen
- Department of Food Safety and Infection Biology, Norwegian University of Life Sciences (NMBU), Pb 8146 Dep., 0033, Oslo, Norway. .,Present address: Nofima AS, Division of Aquaculture, PO Box 210, Ås, N-1431, Norway.
| | - Erik Hjerde
- Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway
| | - Terje Klemetsen
- Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway
| | - Nils Peder Willassen
- Department of Chemistry, Faculty of Science and Technology, University of Tromsø, N-9037, Tromsø, Norway.,The Norwegian Structural Biology Centre, University of Tromsø, N-9037, Tromsø, Norway
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36
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Contreras-Moreira B, Cantalapiedra CP, García-Pereira MJ, Gordon SP, Vogel JP, Igartua E, Casas AM, Vinuesa P. Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species. FRONTIERS IN PLANT SCIENCE 2017; 8:184. [PMID: 28261241 PMCID: PMC5306281 DOI: 10.3389/fpls.2017.00184] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 01/30/2017] [Indexed: 05/22/2023]
Abstract
The pan-genome of a species is defined as the union of all the genes and non-coding sequences found in all its individuals. However, constructing a pan-genome for plants with large genomes is daunting both in sequencing cost and the scale of the required computational analysis. A more affordable alternative is to focus on the genic repertoire by using transcriptomic data. Here, the software GET_HOMOLOGUES-EST was benchmarked with genomic and RNA-seq data of 19 Arabidopsis thaliana ecotypes and then applied to the analysis of transcripts from 16 Hordeum vulgare genotypes. The goal was to sample their pan-genomes and classify sequences as core, if detected in all accessions, or accessory, when absent in some of them. The resulting sequence clusters were used to simulate pan-genome growth, and to compile Average Nucleotide Identity matrices that summarize intra-species variation. Although transcripts were found to under-estimate pan-genome size by at least 10%, we concluded that clusters of expressed sequences can recapitulate phylogeny and reproduce two properties observed in A. thaliana gene models: accessory loci show lower expression and higher non-synonymous substitution rates than core genes. Finally, accessory sequences were observed to preferentially encode transposon components in both species, plus disease resistance genes in cultivated barleys, and a variety of protein domains from other families that appear frequently associated with presence/absence variation in the literature. These results demonstrate that pan-genome analyses are useful to explore germplasm diversity.
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Affiliation(s)
- Bruno Contreras-Moreira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones CientíficasZaragoza, Spain; Fundación ARAIDZaragoza, Spain
| | - Carlos P Cantalapiedra
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - María J García-Pereira
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | | | - John P Vogel
- DOE Joint Genome Institute, Walnut Creek CA, USA
| | - Ernesto Igartua
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Ana M Casas
- Estación Experimental de Aula Dei - Consejo Superior de Investigaciones Científicas Zaragoza, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, Mexico
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