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Tullume-Vergara PO, Caicedo KYO, Tantalean JFC, Serrano MG, Buck GA, Teixeira MMG, Shaw JJ, Alves JMP. Genomes of Endotrypanum monterogeii from Panama and Zelonia costaricensis from Brazil: Expansion of Multigene Families in Leishmaniinae Parasites That Are Close Relatives of Leishmania spp. Pathogens 2023; 12:1409. [PMID: 38133293 PMCID: PMC10747355 DOI: 10.3390/pathogens12121409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/10/2023] [Accepted: 11/24/2023] [Indexed: 12/23/2023] Open
Abstract
The Leishmaniinae subfamily of the Trypanosomatidae contains both genus Zelonia (monoxenous) and Endotrypanum (dixenous). They are amongst the nearest known relatives of Leishmania, which comprises many human pathogens widespread in the developing world. These closely related lineages are models for the genomic biology of monoxenous and dixenous parasites. Herein, we used comparative genomics to identify the orthologous groups (OGs) shared among 26 Leishmaniinae species to investigate gene family expansion/contraction and applied two phylogenomic approaches to confirm relationships within the subfamily. The Endotrypanum monterogeii and Zelonia costaricensis genomes were assembled, with sizes of 29.9 Mb and 38.0 Mb and 9.711 and 12.201 predicted protein-coding genes, respectively. The genome of E. monterogeii displayed a higher number of multicopy cell surface protein families, including glycoprotein 63 and glycoprotein 46, compared to Leishmania spp. The genome of Z. costaricensis presents expansions of BT1 and amino acid transporters and proteins containing leucine-rich repeat domains, as well as a loss of ABC-type transporters. In total, 415 and 85 lineage-specific OGs were identified in Z. costaricensis and E. monterogeii. The evolutionary relationships within the subfamily were confirmed using the supermatrix (3384 protein-coding genes) and supertree methods. Overall, this study showed new expansions of multigene families in monoxenous and dixenous parasites of the subfamily Leishmaniinae.
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Affiliation(s)
- Percy O. Tullume-Vergara
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Kelly Y. O. Caicedo
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Jose F. C. Tantalean
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Myrna G. Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, 1101 E Marshall St., Richmond, VA 23298, USA; (M.G.S.); (G.A.B.)
| | - Gregory A. Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, 1101 E Marshall St., Richmond, VA 23298, USA; (M.G.S.); (G.A.B.)
| | - Marta M. G. Teixeira
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Jeffrey J. Shaw
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
| | - Joao M. P. Alves
- Department of Parasitology, Institute for Biomedical Sciences, University of Sao Paulo, Av. Prof. Lineu Prestes, 1374, Sao Paulo 05508-000, SP, Brazil; (P.O.T.-V.); (K.Y.O.C.); (J.F.C.T.); (M.M.G.T.); (J.J.S.)
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Glascock AL, Jimenez NR, Boundy S, Koparde VN, Brooks JP, Edwards DJ, Strauss Iii JF, Jefferson KK, Serrano MG, Buck GA, Fettweis JM. Unique roles of vaginal Megasphaera phylotypes in reproductive health. Microb Genom 2021; 7. [PMID: 34898422 PMCID: PMC8767330 DOI: 10.1099/mgen.0.000526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The composition of the human vaginal microbiome has been extensively studied and is known to influence reproductive health. However, the functional roles of individual taxa and their contributions to negative health outcomes have yet to be well characterized. Here, we examine two vaginal bacterial taxa grouped within the genus Megasphaera that have been previously associated with bacterial vaginosis (BV) and pregnancy complications. Phylogenetic analyses support the classification of these taxa as two distinct species. These two phylotypes, Megasphaera phylotype 1 (MP1) and Megasphaera phylotype 2 (MP2), differ in genomic structure and metabolic potential, suggestive of differential roles within the vaginal environment. Further, these vaginal taxa show evidence of genome reduction and changes in DNA base composition, which may be common features of host dependence and/or adaptation to the vaginal environment. In a cohort of 3870 women, we observed that MP1 has a stronger positive association with bacterial vaginosis whereas MP2 was positively associated with trichomoniasis. MP1, in contrast to MP2 and other common BV-associated organisms, was not significantly excluded in pregnancy. In a cohort of 52 pregnant women, MP1 was both present and transcriptionally active in 75.4 % of vaginal samples. Conversely, MP2 was largely absent in the pregnant cohort. This study provides insight into the evolutionary history, genomic potential and predicted functional role of two clinically relevant vaginal microbial taxa.
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Affiliation(s)
| | - Nicole R Jimenez
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Sam Boundy
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Vishal N Koparde
- Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - J Paul Brooks
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Supply Chain Management and Analytics, Virginia Commonwealth University, Richmond, VA, USA
| | - David J Edwards
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, VA, USA
| | - Jerome F Strauss Iii
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, USA
| | - Kimberly K Jefferson
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, USA
| | - Myrna G Serrano
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A Buck
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Computer Science, Virginia Commonwealth University, Richmond, VA, USA
| | - Jennifer M Fettweis
- Department of Microbiology & Immunology, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, VA, USA
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3
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Kumar M, Singh P, Murugesan S, Vetizou M, McCulloch J, Badger JH, Trinchieri G, Al Khodor S. Microbiome as an Immunological Modifier. Methods Mol Biol 2020; 2055:595-638. [PMID: 31502171 PMCID: PMC8276114 DOI: 10.1007/978-1-4939-9773-2_27] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Humans are living ecosystems composed of human cells and microbes. The microbiome is the collection of microbes (microbiota) and their genes. Recent breakthroughs in the high-throughput sequencing technologies have made it possible for us to understand the composition of the human microbiome. Launched by the National Institutes of Health in USA, the human microbiome project indicated that our bodies harbor a wide array of microbes, specific to each body site with interpersonal and intrapersonal variabilities. Numerous studies have indicated that several factors influence the development of the microbiome including genetics, diet, use of antibiotics, and lifestyle, among others. The microbiome and its mediators are in a continuous cross talk with the host immune system; hence, any imbalance on one side is reflected on the other. Dysbiosis (microbiota imbalance) was shown in many diseases and pathological conditions such as inflammatory bowel disease, celiac disease, multiple sclerosis, rheumatoid arthritis, asthma, diabetes, and cancer. The microbial composition mirrors inflammation variations in certain disease conditions, within various stages of the same disease; hence, it has the potential to be used as a biomarker.
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Affiliation(s)
- Manoj Kumar
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Parul Singh
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Selvasankar Murugesan
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar
| | - Marie Vetizou
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John McCulloch
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan H Badger
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Giorgio Trinchieri
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Souhaila Al Khodor
- Division of Translational Medicine, Research Department, Sidra Medicine, Doha, Qatar.
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Fettweis JM, Serrano MG, Brooks JP, Edwards DJ, Girerd PH, Parikh HI, Huang B, Arodz TJ, Edupuganti L, Glascock AL, Xu J, Jimenez NR, Vivadelli SC, Fong SS, Sheth NU, Jean S, Lee V, Bokhari YA, Lara AM, Mistry SD, Duckworth RA, Bradley SP, Koparde VN, Orenda XV, Milton SH, Rozycki SK, Matveyev AV, Wright ML, Huzurbazar SV, Jackson EM, Smirnova E, Korlach J, Tsai YC, Dickinson MR, Brooks JL, Drake JI, Chaffin DO, Sexton AL, Gravett MG, Rubens CE, Wijesooriya NR, Hendricks-Muñoz KD, Jefferson KK, Strauss JF, Buck GA. The vaginal microbiome and preterm birth. Nat Med 2019; 25:1012-1021. [PMID: 31142849 PMCID: PMC6750801 DOI: 10.1038/s41591-019-0450-2] [Citation(s) in RCA: 470] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/09/2019] [Indexed: 12/15/2022]
Abstract
The incidence of preterm birth exceeds 10% worldwide. There are significant disparities in the frequency of preterm birth among populations within countries, and women of African ancestry disproportionately bear the burden of risk in the United States. In the present study, we report a community resource that includes ‘omics’ data from approximately 12,000 samples as part of the integrative Human Microbiome Project. Longitudinal analyses of 16S ribosomal RNA, metagenomic, metatranscriptomic and cytokine profiles from 45 preterm and 90 term birth controls identified harbingers of preterm birth in this cohort of women predominantly of African ancestry. Women who delivered preterm exhibited significantly lower vaginal levels of Lactobacillus crispatus and higher levels of BVAB1, Sneathia amnii, TM7-H1, a group of Prevotella species and nine additional taxa. The first representative genomes of BVAB1 and TM7-H1 are described. Preterm-birth-associated taxa were correlated with proinflammatory cytokines in vaginal fluid. These findings highlight new opportunities for assessment of the risk of preterm birth. As part of the second phase of Human Microbiome Project, the Multi-Omic Microbiome Study: Pregnancy Initiative presents a community resource to help better understand how microbiome and host profiles change throughout pregnancy as well as to identify new opportunities for assessment of the risk of preterm birth.
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Affiliation(s)
- Jennifer M Fettweis
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Myrna G Serrano
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - J Paul Brooks
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Supply Chain Management and Analytics, School of Business, Virginia Commonwealth University, Richmond, VA, USA
| | - David J Edwards
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Statistical Sciences and Operations Research, College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Philippe H Girerd
- Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Hardik I Parikh
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Bernice Huang
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Tom J Arodz
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Laahirie Edupuganti
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Jie Xu
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Division of Neonatal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Department of Pediatrics, School of Medicine, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Nicole R Jimenez
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Stephany C Vivadelli
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Stephen S Fong
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Department of Chemical and Life Science Engineering, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Nihar U Sheth
- Center for the Study of Biological Complexity, VCU Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - Sophonie Jean
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir Lee
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Yahya A Bokhari
- Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA
| | - Ana M Lara
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Shreni D Mistry
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Robert A Duckworth
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Steven P Bradley
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Vishal N Koparde
- Center for the Study of Biological Complexity, VCU Life Sciences, Virginia Commonwealth University, Richmond, VA, USA
| | - X Valentine Orenda
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Sarah H Milton
- Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Sarah K Rozycki
- School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrey V Matveyev
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Michelle L Wright
- Nell Hodgson Woodruff School of Nursing, Emory University, Atlanta, GA, USA.,Department of Women's Health, Dell School of Medicine, University of Texas at Austin, Austin, TX, USA.,School of Nursing, University of Texas at Austin, Austin, TX, USA
| | - Snehalata V Huzurbazar
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, WV, USA
| | - Eugenie M Jackson
- Department of Biostatistics, School of Public Health, West Virginia University, Morgantown, WV, USA
| | - Ekaterina Smirnova
- Department of Mathematical Sciences, University of Montana, Missoula, MT, USA.,Department of Biostatistics, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | | | | | - Molly R Dickinson
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Jamie L Brooks
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Jennifer I Drake
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - Donald O Chaffin
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA
| | - Amber L Sexton
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA
| | - Michael G Gravett
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA.,Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA
| | - Craig E Rubens
- Global Alliance to Prevent Prematurity and Stillbirth, Seattle, WA, USA
| | - N Romesh Wijesooriya
- Department of Pediatrics, School of Medicine, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Karen D Hendricks-Muñoz
- Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA.,Division of Neonatal Medicine, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Department of Pediatrics, School of Medicine, Children's Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Kimberly K Jefferson
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA.,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA
| | - Gregory A Buck
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, VA, USA. .,Center for Microbiome Engineering and Data Analysis, Virginia Commonwealth University, Richmond, VA, USA. .,Department of Computer Science, College of Engineering, Virginia Commonwealth University, Richmond, VA, USA.
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5
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Bradwell KR, Koparde VN, Matveyev AV, Serrano MG, Alves JMP, Parikh H, Huang B, Lee V, Espinosa-Alvarez O, Ortiz PA, Costa-Martins AG, Teixeira MMG, Buck GA. Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence. BMC Genomics 2018; 19:770. [PMID: 30355302 PMCID: PMC6201504 DOI: 10.1186/s12864-018-5112-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 09/25/2018] [Indexed: 01/09/2023] Open
Abstract
Background Trypanosoma conorhini and Trypanosoma rangeli, like Trypanosoma cruzi, are kinetoplastid protist parasites of mammals displaying divergent hosts, geographic ranges and lifestyles. Largely nonpathogenic T. rangeli and T. conorhini represent clades that are phylogenetically closely related to the T. cruzi and T. cruzi-like taxa and provide insights into the evolution of pathogenicity in those parasites. T. rangeli, like T. cruzi is endemic in many Latin American countries, whereas T. conorhini is tropicopolitan. T. rangeli and T. conorhini are exclusively extracellular, while T. cruzi has an intracellular stage in the mammalian host. Results Here we provide the first comprehensive sequence analysis of T. rangeli AM80 and T. conorhini 025E, and provide a comparison of their genomes to those of T. cruzi G and T. cruzi CL, respectively members of T. cruzi lineages TcI and TcVI. We report de novo assembled genome sequences of the low-virulent T. cruzi G, T. rangeli AM80, and T. conorhini 025E ranging from ~ 21–25 Mbp, with ~ 10,000 to 13,000 genes, and for the highly virulent and hybrid T. cruzi CL we present a ~ 65 Mbp in-house assembled haplotyped genome with ~ 12,500 genes per haplotype. Single copy orthologs of the two T. cruzi strains exhibited ~ 97% amino acid identity, and ~ 78% identity to proteins of T. rangeli or T. conorhini. Proteins of the latter two organisms exhibited ~ 84% identity. T. cruzi CL exhibited the highest heterozygosity. T. rangeli and T. conorhini displayed greater metabolic capabilities for utilization of complex carbohydrates, and contained fewer retrotransposons and multigene family copies, i.e. trans-sialidases, mucins, DGF-1, and MASP, compared to T. cruzi. Conclusions Our analyses of the T. rangeli and T. conorhini genomes closely reflected their phylogenetic proximity to the T. cruzi clade, and were largely consistent with their divergent life cycles. Our results provide a greater context for understanding the life cycles, host range expansion, immunity evasion, and pathogenesis of these trypanosomatids. Electronic supplementary material The online version of this article (10.1186/s12864-018-5112-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katie R Bradwell
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Present address: Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - Vishal N Koparde
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
| | - Andrey V Matveyev
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Myrna G Serrano
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - João M P Alves
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | - Hardik Parikh
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Bernice Huang
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA.,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA
| | - Vladimir Lee
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
| | | | - Paola A Ortiz
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | | | - Marta M G Teixeira
- Department of Parasitology, ICB, University of São Paulo, São Paulo, SP, Brazil
| | - Gregory A Buck
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA. .,Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA, USA.
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6
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The reduced genome of Candidatus Kinetoplastibacterium sorsogonicusi, the endosymbiont of Kentomonas sorsogonicus (Trypanosomatidae): loss of the haem-synthesis pathway. Parasitology 2018; 145:1287-1293. [PMID: 29642956 DOI: 10.1017/s003118201800046x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Trypanosomatids of the genera Angomonas and Strigomonas (subfamily Strigomonadinae) have long been known to contain intracellular beta-proteobacteria, which provide them with many important nutrients such as haem, essential amino acids and vitamins. Recently, Kentomonas sorsogonicus, a divergent member of Strigomonadinae, has been described. Herein, we characterize the genome of its endosymbiont, Candidatus Kinetoplastibacterium sorsogonicusi. This genome is completely syntenic with those of other known Ca. Kinetoplastibacterium spp., but more reduced in size (~742 kb, compared with 810-833 kb, respectively). Gene losses are not concentrated in any hot-spots but are instead distributed throughout the genome. The most conspicuous loss is that of the haem-synthesis pathway. For long, removing haemin from the culture medium has been a standard procedure in cultivating trypanosomatids isolated from insects; continued growth was considered as an evidence of endosymbiont presence. However, we demonstrate that, despite bearing the endosymbiont, K. sorsogonicus cannot grow in culture without haem. Thus, the traditional test cannot be taken as a reliable criterion for the absence or presence of endosymbionts in trypanosomatid flagellates. It remains unclear why the ability to synthesize such an essential compound was lost in Ca. K. sorsogonicusi, whereas all other known bacterial endosymbionts of trypanosomatids retain them.
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7
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Teh BS, Lau NS, Ng FL, Abdul Rahman AY, Wan X, Saito JA, Hou S, Teh AH, Najimudin N, Alam M. Complete genome sequence of the thermophilic Thermus sp. CCB_US3_UF1 from a hot spring in Malaysia. Stand Genomic Sci 2015; 10:76. [PMID: 26457128 PMCID: PMC4599208 DOI: 10.1186/s40793-015-0053-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 07/28/2015] [Indexed: 02/08/2023] Open
Abstract
Thermus sp. strain CCB_US3_UF1 is a thermophilic bacterium of the genus Thermus, a member of the family Thermaceae. Members of the genus Thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1 isolated from a hot spring in Malaysia, which is the fifth member of the genus Thermus with a completely sequenced and publicly available genome (Genbank date of release: December 2, 2011). Thermus sp. CCB_US3_UF1 has the third largest genome within the genus. The complete genome comprises of a chromosome of 2.26 Mb and a plasmid of 19.7 kb. The genome contains 2279 protein-coding and 54 RNA genes. In addition, its genome revealed potential pathways for the synthesis of secondary metabolites (isoprenoid) and pigments (carotenoid).
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Affiliation(s)
- Beng Soon Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia ; Present address: Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Nyok-Sean Lau
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Fui Ling Ng
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Xuehua Wan
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Jennifer A Saito
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA
| | - Aik-Hong Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Nazalan Najimudin
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Maqsudul Alam
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii USA ; Department of Microbiology, University of Hawaii, Honolulu, Hawaii USA
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8
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The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 2015; 16:276-89. [PMID: 25211071 PMCID: PMC5109542 DOI: 10.1016/j.chom.2014.08.014] [Citation(s) in RCA: 310] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Much has been learned about the diversity and distribution of human-associated microbial communities, but we still know little about the biology of the microbiome, how it interacts with the host, and how the host responds to its resident microbiota. The Integrative Human Microbiome Project (iHMP, http://hmp2.org), the second phase of the NIH Human Microbiome Project, will study these interactions by analyzing microbiome and host activities in longitudinal studies of disease-specific cohorts and by creating integrated data sets of microbiome and host functional properties. These data sets will serve as experimental test beds to evaluate new models, methods, and analyses on the interactions of host and microbiome. Here we describe the three models of microbiome-associated human conditions, on the dynamics of preterm birth, inflammatory bowel disease, and type 2 diabetes, and their underlying hypotheses, as well as the multi-omic data types to be collected, integrated, and distributed through public repositories as a community resource.
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Fettweis JM, Serrano MG, Huang B, Brooks JP, Glascock AL, Sheth NU, Strauss JF, Jefferson KK, Buck GA. An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease. PLoS One 2014; 9:e110943. [PMID: 25337710 PMCID: PMC4206474 DOI: 10.1371/journal.pone.0110943] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
Humans are colonized by thousands of bacterial species, but it is difficult to assess the metabolic and pathogenic potential of the majority of these because they have yet to be cultured. Here, we characterize an uncultivated vaginal mycoplasma tightly associated with trichomoniasis that was previously known by its 16S rRNA sequence as "Mnola." In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease. The genomes of four strains of this species were reconstructed using metagenome sequencing and assembly of DNA from four discrete mid-vaginal samples, one of which was obtained from a pregnant woman with trichomoniasis who delivered prematurely. These bacteria harbor several putative virulence factors and display unique metabolic strategies. Genes encoding proteins with high similarity to potential virulence factors include two collagenases, a hemolysin, an O-sialoglycoprotein endopeptidase and a feoB-type ferrous iron transport system. We propose the name "Candidatus Mycoplasma girerdii" for this potential new pathogen.
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Affiliation(s)
- Jennifer M. Fettweis
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail:
| | - Myrna G. Serrano
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Bernice Huang
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - J. Paul Brooks
- Department of Statistical Sciences and Operations Research, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Abigail L. Glascock
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Nihar U. Sheth
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | | | - Jerome F. Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Kimberly K. Jefferson
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Gregory A. Buck
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, Virginia, United States of America
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, United States of America
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Pasternak Z, Njagi M, Shani Y, Chanyi R, Rotem O, Lurie-Weinberger MN, Koval S, Pietrokovski S, Gophna U, Jurkevitch E. In and out: an analysis of epibiotic vs periplasmic bacterial predators. THE ISME JOURNAL 2014; 8:625-635. [PMID: 24088628 PMCID: PMC3930308 DOI: 10.1038/ismej.2013.164] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 07/14/2013] [Accepted: 08/17/2013] [Indexed: 01/17/2023]
Abstract
Bdellovibrio and like organisms (BALO) are obligate predators of Gram-negative bacteria, belonging to the α- and δ-proteobacteria. BALO prey using either a periplasmic or an epibiotic predatory strategy, but the genetic background underlying these phenotypes is not known. Here we compare the epibiotic Bdellovibrio exovorus and Micavibrio aeruginosavorus to the periplasmic B. bacteriovorus and Bacteriovorax marinus. Electron microscopy showed that M. aeruginosavorus, but not B. exovorus, can attach to prey cells in a non-polar manner through its longitudinal side. Both these predators were resistant to a surprisingly high number of antibiotic compounds, possibly via 26 and 19 antibiotic-resistance genes, respectively, most of them encoding efflux pumps. Comparative genomic analysis of all the BALOs revealed that epibiotic predators have a much smaller genome (ca. 2.5 Mbp) than the periplasmic predators (ca. 3.5 Mbp). Additionally, periplasmic predators have, on average, 888 more proteins, at least 60% more peptidases, and one more rRNA operon. Fifteen and 219 protein families were specific to the epibiotic and the periplasmic predators, respectively, the latter clearly forming the core of the periplasmic 'predatome', which is upregulated during the growth phase. Metabolic deficiencies of epibiotic genomes include the synthesis of inosine, riboflavin, vitamin B6 and the siderophore aerobactin. The phylogeny of the epibiotic predators suggests that they evolved by convergent evolution, with M. aeruginosavorus originating from a non-predatory ancestor while B. exovorus evolved from periplasmic predators by gene loss.
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Affiliation(s)
- Z Pasternak
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel.
| | - M Njagi
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - Y Shani
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - R Chanyi
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - O Rotem
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
| | - M N Lurie-Weinberger
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - S Koval
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - S Pietrokovski
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - U Gophna
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - E Jurkevitch
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
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11
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Klein CC, Alves JMP, Serrano MG, Buck GA, Vasconcelos ATR, Sagot MF, Teixeira MMG, Camargo EP, Motta MCM. Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses. PLoS One 2013; 8:e79786. [PMID: 24260300 PMCID: PMC3833962 DOI: 10.1371/journal.pone.0079786] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 09/25/2013] [Indexed: 12/03/2022] Open
Abstract
Some non-pathogenic trypanosomatids maintain a mutualistic relationship with a betaproteobacterium of the Alcaligenaceae family. Intensive nutritional exchanges have been reported between the two partners, indicating that these protozoa are excellent biological models to study metabolic co-evolution. We previously sequenced and herein investigate the entire genomes of five trypanosomatids which harbor a symbiotic bacterium (SHTs for Symbiont-Haboring Trypanosomatids) and the respective bacteria (TPEs for Trypanosomatid Proteobacterial Endosymbiont), as well as two trypanosomatids without symbionts (RTsfor Regular Trypanosomatids), for the presence of genes of the classical pathways for vitamin biosynthesis. Our data show that genes for the biosynthetic pathways of thiamine, biotin, and nicotinic acid are absent from all trypanosomatid genomes. This is in agreement with the absolute growth requirement for these vitamins in all protozoa of the family. Also absent from the genomes of RTs are the genes for the synthesis of pantothenic acid, folic acid, riboflavin, and vitamin B6. This is also in agreement with the available data showing that RTs are auxotrophic for these essential vitamins. On the other hand, SHTs are autotrophic for such vitamins. Indeed, all the genes of the corresponding biosynthetic pathways were identified, most of them in the symbiont genomes, while a few genes, mostly of eukaryotic origin, were found in the host genomes. The only exceptions to the latter are: the gene coding for the enzyme ketopantoate reductase (EC:1.1.1.169) which is related instead to the Firmicutes bacteria; and two other genes, one involved in the salvage pathway of pantothenic acid and the other in the synthesis of ubiquinone, that are related to Gammaproteobacteria. Their presence in trypanosomatids may result from lateral gene transfer. Taken together, our results reinforce the idea that the low nutritional requirement of SHTs is associated with the presence of the symbiotic bacterium, which contains most genes for vitamin production.
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Affiliation(s)
- Cecilia C. Klein
- BAMBOO Team, INRIA Grenoble-Rhône-Alpes, Villeurbanne, France
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France
- Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil
- * E-mail: (CCK); (MCMM)
| | - João M. P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Myrna G. Serrano
- Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Gregory A. Buck
- Virginia Commonwealth University, Richmond, Virginia, United States of America
| | | | - Marie-France Sagot
- BAMBOO Team, INRIA Grenoble-Rhône-Alpes, Villeurbanne, France
- Laboratoire Biométrie et Biologie Evolutive, Université de Lyon, Université Lyon 1, CNRS, UMR5558, Villeurbanne, France
| | - Marta M. G. Teixeira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Erney P. Camargo
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria Cristina M. Motta
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (CCK); (MCMM)
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12
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Alves JMP, Klein CC, da Silva FM, Costa-Martins AG, Serrano MG, Buck GA, Vasconcelos ATR, Sagot MF, Teixeira MMG, Motta MCM, Camargo EP. Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. BMC Evol Biol 2013; 13:190. [PMID: 24015778 PMCID: PMC3846528 DOI: 10.1186/1471-2148-13-190] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosomatids of the genera Angomonas and Strigomonas live in a mutualistic association characterized by extensive metabolic cooperation with obligate endosymbiotic Betaproteobacteria. However, the role played by the symbiont has been more guessed by indirect means than evidenced. Symbiont-harboring trypanosomatids, in contrast to their counterparts lacking symbionts, exhibit lower nutritional requirements and are autotrophic for essential amino acids. To evidence the symbiont's contributions to this autotrophy, entire genomes of symbionts and trypanosomatids with and without symbionts were sequenced here. RESULTS Analyses of the essential amino acid pathways revealed that most biosynthetic routes are in the symbiont genome. By contrast, the host trypanosomatid genome contains fewer genes, about half of which originated from different bacterial groups, perhaps only one of which (ornithine cyclodeaminase, EC:4.3.1.12) derived from the symbiont. Nutritional, enzymatic, and genomic data were jointly analyzed to construct an integrated view of essential amino acid metabolism in symbiont-harboring trypanosomatids. This comprehensive analysis showed perfect concordance among all these data, and revealed that the symbiont contains genes for enzymes that complete essential biosynthetic routes for the host amino acid production, thus explaining the low requirement for these elements in symbiont-harboring trypanosomatids. Phylogenetic analyses show that the cooperation between symbionts and their hosts is complemented by multiple horizontal gene transfers, from bacterial lineages to trypanosomatids, that occurred several times in the course of their evolution. Transfers occur preferentially in parts of the pathways that are missing from other eukaryotes. CONCLUSION We have herein uncovered the genetic and evolutionary bases of essential amino acid biosynthesis in several trypanosomatids with and without endosymbionts, explaining and complementing decades of experimental results. We uncovered the remarkable plasticity in essential amino acid biosynthesis pathway evolution in these protozoans, demonstrating heavy influence of horizontal gene transfer events, from Bacteria to trypanosomatid nuclei, in the evolution of these pathways.
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13
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Alves JMP, Serrano MG, Maia da Silva F, Voegtly LJ, Matveyev AV, Teixeira MMG, Camargo EP, Buck GA. Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. Genome Biol Evol 2013; 5:338-50. [PMID: 23345457 PMCID: PMC3590767 DOI: 10.1093/gbe/evt012] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It has been long known that insect-infecting trypanosomatid flagellates from the genera Angomonas and Strigomonas harbor bacterial endosymbionts (Candidatus Kinetoplastibacterium or TPE [trypanosomatid proteobacterial endosymbiont]) that supplement the host metabolism. Based on previous analyses of other bacterial endosymbiont genomes from other lineages, a stereotypical path of genome evolution in such bacteria over the duration of their association with the eukaryotic host has been characterized. In this work, we sequence and analyze the genomes of five TPEs, perform their metabolic reconstruction, do an extensive phylogenomic analyses with all available Betaproteobacteria, and compare the TPEs with their nearest betaproteobacterial relatives. We also identify a number of housekeeping and central metabolism genes that seem to have undergone positive selection. Our genome structure analyses show total synteny among the five TPEs despite millions of years of divergence, and that this lineage follows the common path of genome evolution observed in other endosymbionts of diverse ancestries. As previously suggested by cell biology and biochemistry experiments, Ca. Kinetoplastibacterium spp. preferentially maintain those genes necessary for the biosynthesis of compounds needed by their hosts. We have also shown that metabolic and informational genes related to the cooperation with the host are overrepresented amongst genes shown to be under positive selection. Finally, our phylogenomic analysis shows that, while being in the Alcaligenaceae family of Betaproteobacteria, the closest relatives of these endosymbionts are not in the genus Bordetella as previously reported, but more likely in the Taylorella genus.
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Affiliation(s)
- João M P Alves
- Department of Microbiology and Immunology and the Center for the Study of Biological Complexity, Virginia Commonwealth University, VA, USA.
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14
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Ong SY, Pratap CB, Wan X, Hou S, Rahman AYA, Saito JA, Nath G, Alam M. The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12. Stand Genomic Sci 2013; 7:483-96. [PMID: 24019994 PMCID: PMC3764930 DOI: 10.4056/sigs.3286690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative, facultatively anaerobic bacterium. It belongs to the family Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of residing in the human gallbladder by forming a biofilm and hence causing the person to become a typhoid carrier. Here we present the complete genome of Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was isolated from a chronic carrier in Varanasi, India. The complete genome comprises a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella enterica serovar Typhi strain CT18, although their genome structure is slightly different.
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Affiliation(s)
- Su Yean Ong
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
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15
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Harwich MD, Serrano MG, Fettweis JM, Alves JMP, Reimers MA, Buck GA, Jefferson KK. Genomic sequence analysis and characterization of Sneathia amnii sp. nov. BMC Genomics 2012; 13 Suppl 8:S4. [PMID: 23281612 PMCID: PMC3535699 DOI: 10.1186/1471-2164-13-s8-s4] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacteria of the genus Sneathia are emerging as potential pathogens of the female reproductive tract. Species of Sneathia, which were formerly grouped with Leptotrichia, can be part of the normal microbiota of the genitourinary tracts of men and women, but they are also associated with a variety of clinical conditions including bacterial vaginosis, preeclampsia, preterm labor, spontaneous abortion, post-partum bacteremia and other invasive infections. Sneathia species also exhibit a significant correlation with sexually transmitted diseases and cervical cancer. Because Sneathia species are fastidious and rarely cultured successfully in vitro; and the genomes of members of the genus had until now not been characterized, very little is known about the physiology or the virulence of these organisms. RESULTS Here, we describe a novel species, Sneathia amnii sp. nov, which closely resembles bacteria previously designated "Leptotrichia amnionii". As part of the Vaginal Human Microbiome Project at VCU, a vaginal isolate of S. amnii sp. nov. was identified, successfully cultured and bacteriologically cloned. The biochemical characteristics and virulence properties of the organism were examined in vitro, and the genome of the organism was sequenced, annotated and analyzed. The analysis revealed a reduced circular genome of ~1.34 Mbp, containing ~1,282 protein-coding genes. Metabolic reconstruction of the bacterium reflected its biochemical phenotype, and several genes potentially associated with pathogenicity were identified. CONCLUSIONS Bacteria with complex growth requirements frequently remain poorly characterized and, as a consequence, their roles in health and disease are unclear. Elucidation of the physiology and identification of genes putatively involved in the metabolism and virulence of S. amnii may lead to a better understanding of the role of this potential pathogen in bacterial vaginosis, preterm birth, and other issues associated with vaginal and reproductive health.
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Affiliation(s)
- Michael D Harwich
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, 1101 E. Marshall Street - PO Box 980678, Richmond, VA 23298-0678, USA
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16
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Pasternak Z, Pietrokovski S, Rotem O, Gophna U, Lurie-Weinberger MN, Jurkevitch E. By their genes ye shall know them: genomic signatures of predatory bacteria. ISME JOURNAL 2012. [PMID: 23190728 DOI: 10.1038/ismej.2012.149] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Predatory bacteria are taxonomically disparate, exhibit diverse predatory strategies and are widely distributed in varied environments. To date, their predatory phenotypes cannot be discerned in genome sequence data thereby limiting our understanding of bacterial predation, and of its impact in nature. Here, we define the 'predatome,' that is, sets of protein families that reflect the phenotypes of predatory bacteria. The proteomes of all sequenced 11 predatory bacteria, including two de novo sequenced genomes, and 19 non-predatory bacteria from across the phylogenetic and ecological landscapes were compared. Protein families discriminating between the two groups were identified and quantified, demonstrating that differences in the proteomes of predatory and non-predatory bacteria are large and significant. This analysis allows predictions to be made, as we show by confirming from genome data an over-looked bacterial predator. The predatome exhibits deficiencies in riboflavin and amino acids biosynthesis, suggesting that predators obtain them from their prey. In contrast, these genomes are highly enriched in adhesins, proteases and particular metabolic proteins, used for binding to, processing and consuming prey, respectively. Strikingly, predators and non-predators differ in isoprenoid biosynthesis: predators use the mevalonate pathway, whereas non-predators, like almost all bacteria, use the DOXP pathway. By defining predatory signatures in bacterial genomes, the predatory potential they encode can be uncovered, filling an essential gap for measuring bacterial predation in nature. Moreover, we suggest that full-genome proteomic comparisons are applicable to other ecological interactions between microbes, and provide a convenient and rational tool for the functional classification of bacteria.
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Affiliation(s)
- Zohar Pasternak
- Department of Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel.
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17
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Complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12. J Bacteriol 2012; 194:2115-6. [PMID: 22461552 DOI: 10.1128/jb.00121-12] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We report here the complete genome sequence of Salmonella enterica subsp. enterica serovar Typhi P-stx-12, a clinical isolate obtained from a typhoid carrier in India.
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18
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Voigt A, Schöfl G, Saluz HP. The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens. PLoS One 2012; 7:e35097. [PMID: 22506068 PMCID: PMC3323650 DOI: 10.1371/journal.pone.0035097] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 03/08/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Chlamydiaceae are a family of obligate intracellular pathogens causing a wide range of diseases in animals and humans, and facing unique evolutionary constraints not encountered by free-living prokaryotes. To investigate genomic aspects of infection, virulence and host preference we have sequenced Chlamydia psittaci, the pathogenic agent of ornithosis. RESULTS A comparison of the genome of the avian Chlamydia psittaci isolate 6BC with the genomes of other chlamydial species, C. trachomatis, C. muridarum, C. pneumoniae, C. abortus, C. felis and C. caviae, revealed a high level of sequence conservation and synteny across taxa, with the major exception of the human pathogen C. trachomatis. Important differences manifest in the polymorphic membrane protein family specific for the Chlamydiae and in the highly variable chlamydial plasticity zone. We identified a number of psittaci-specific polymorphic membrane proteins of the G family that may be related to differences in host-range and/or virulence as compared to closely related Chlamydiaceae. We calculated non-synonymous to synonymous substitution rate ratios for pairs of orthologous genes to identify putative targets of adaptive evolution and predicted type III secreted effector proteins. CONCLUSIONS This study is the first detailed analysis of the Chlamydia psittaci genome sequence. It provides insights in the genome architecture of C. psittaci and proposes a number of novel candidate genes mostly of yet unknown function that may be important for pathogen-host interactions.
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Affiliation(s)
- Anja Voigt
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Gerhard Schöfl
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
| | - Hans Peter Saluz
- Leibniz-Institute for Natural Product Research and Infection Biology, Jena, Germany
- Friedrich Schiller University, Jena, Germany
- * E-mail:
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19
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Zhang D, Lax AR, Henrissat B, Coutinho P, Katiya N, Nierman WC, Fedorova N. Carbohydrate-active enzymes revealed in Coptotermes formosanus (Isoptera: Rhinotermitidae) transcriptome. INSECT MOLECULAR BIOLOGY 2012; 21:235-245. [PMID: 22243654 DOI: 10.1111/j.1365-2583.2011.01130.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Coptotermes formosanus is one of the most destructive wood-feeding termites. To understand the molecular mechanisms that regulate the development of the termite, a normalized C. formosanus cDNA library was constructed using mixed RNA isolated from workers, soldiers, nymphs and alates of both sexes. The sequencing of this library generated 131 636 expressed sequence tags (ESTs) and 25 939 assembled unigenes. The carbohydrate-active enzymes (CAZymes) revealed in this library were analysed in the present report. A total of 509 putative CAZymes were identified. Diverse cellulolytic enzymes were uncovered from both the host termite and from symbionts harboured by the termite, which were possibly the result of the high efficiency of cellulose utilization. CAZymes associated with trehalose biosynthetic and metabolic pathways were also identified, which are potential regulators of the physiological activities of trehalose, an important insect blood sugar. Representative CAZyme coding genes in glycoside hydrolase family 1 (GH1) were quantitatively analysed. The results showed that the five GH1 β-glucosidase genes were expressed differentially among different castes and one of them was female alate-specific. Overall, the normalized EST library provides a comprehensive genetic resource of C. formosanus and will serve a diverse range of research areas. The CAZymes represent one of the repositories of enzymes useful for physiological studies and applications in sugar-based biofuel production.
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Affiliation(s)
- Dunhua Zhang
- Southern Regional Research Center, ARS, USDA, New Orleans, LA 70124, USA.
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20
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Complete genome sequence of the thermophilic bacterium Geobacillus thermoleovorans CCB_US3_UF5. J Bacteriol 2012; 194:1239. [PMID: 22328744 DOI: 10.1128/jb.06580-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geobacillus thermoleovorans CCB_US3_UF5 is a thermophilic bacterium isolated from a hot spring in Malaysia. Here, we report the complete genome of G. thermoleovorans CCB_US3_UF5, which shows high similarity to the genome of Geobacillus kaustophilus HTA 426 in terms of synteny and orthologous genes.
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21
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Teh BS, Abdul Rahman AY, Saito JA, Hou S, Alam M. Complete genome sequence of the thermophilic bacterium Thermus sp. strain CCB_US3_UF1. J Bacteriol 2012; 194:1240. [PMID: 22328745 PMCID: PMC3294796 DOI: 10.1128/jb.06589-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 12/12/2011] [Indexed: 11/20/2022] Open
Abstract
Thermus sp. strain CCB_US3_UF1, a thermophilic bacterium, has been isolated from a hot spring in Malaysia. Here, we present the complete genome sequence of Thermus sp. CCB_US3_UF1.
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Affiliation(s)
- Beng Soon Teh
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Jennifer A. Saito
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
| | - Shaobin Hou
- Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, Hawaii, USA
| | - Maqsudul Alam
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
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Kemen E, Gardiner A, Schultz-Larsen T, Kemen AC, Balmuth AL, Robert-Seilaniantz A, Bailey K, Holub E, Studholme DJ, MacLean D, Jones JDG. Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol 2011; 9:e1001094. [PMID: 21750662 PMCID: PMC3130010 DOI: 10.1371/journal.pbio.1001094] [Citation(s) in RCA: 213] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Accepted: 05/10/2011] [Indexed: 01/21/2023] Open
Abstract
Biotrophic eukaryotic plant pathogens require a living host for their growth and form an intimate haustorial interface with parasitized cells. Evolution to biotrophy occurred independently in fungal rusts and powdery mildews, and in oomycete white rusts and downy mildews. Biotroph evolution and molecular mechanisms of biotrophy are poorly understood. It has been proposed, but not shown, that obligate biotrophy results from (i) reduced selection for maintenance of biosynthetic pathways and (ii) gain of mechanisms to evade host recognition or suppress host defence. Here we use Illumina sequencing to define the genome, transcriptome, and gene models for the obligate biotroph oomycete and Arabidopsis parasite, Albugo laibachii. A. laibachii is a member of the Chromalveolata, which incorporates Heterokonts (containing the oomycetes), Apicomplexa (which includes human parasites like Plasmodium falciparum and Toxoplasma gondii), and four other taxa. From comparisons with other oomycete plant pathogens and other chromalveolates, we reveal independent loss of molybdenum-cofactor-requiring enzymes in downy mildews, white rusts, and the malaria parasite P. falciparum. Biotrophy also requires “effectors” to suppress host defence; we reveal RXLR and Crinkler effectors shared with other oomycetes, and also discover and verify a novel class of effectors, the “CHXCs”, by showing effector delivery and effector functionality. Our findings suggest that evolution to progressively more intimate association between host and parasite results in reduced selection for retention of certain biosynthetic pathways, and particularly reduced selection for retention of molybdopterin-requiring biosynthetic pathways. These mechanisms are not only relevant to plant pathogenic oomycetes but also to human pathogens within the Chromalveolata. Plant pathogens that cannot grow except on their hosts are called obligate biotrophs. How such biotrophy evolves is poorly understood. In this study, we sequenced the genome of the obligate biotroph white rust pathogen (Albugo laibachii, Oomycota) of Arabidopsis. From comparisons with other oomycete plant pathogens, diatoms, and the human pathogen Plasmodium falciparum, we reveal a loss of important metabolic enzymes. We also reveal the appearance of defence-suppressing “effectors”, some carrying motifs known from other oomycete effectors, and discover and experimentally verify a novel class of effectors that share a CHXC motif within 50 amino acids of the signal peptide cleavage site. Obligate biotrophy involves an intimate association within host cells at the haustorial interface (where the parasite penetrates the host cell's cell wall), where nutrients are acquired from the host and effectors are delivered to the host. We found that A. laibachii, like Hyaloperonospora arabidopsidis and Plasmodium falciparum, lacks molybdopterin-requiring biosynthetic pathways, suggesting relaxed selection for retention of, or even selection against, this pathway. We propose that when defence suppression becomes sufficiently effective, hosts become such a reliable source of nutrients that a free-living phase can be lost. These mechanisms leading to obligate biotrophy and host specificity are relevant not only to plant pathogenic oomycetes but also to human pathogens.
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Affiliation(s)
- Eric Kemen
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Anastasia Gardiner
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | | | - Ariane C. Kemen
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Alexi L. Balmuth
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- The GenePool, The University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kate Bailey
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Eric Holub
- School of Life Sciences, University of Warwick, Wellesbourne Campus, United Kingdom
| | | | - Dan MacLean
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Jonathan D. G. Jones
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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23
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DREAMS of metabolism. Trends Biotechnol 2010; 28:501-8. [DOI: 10.1016/j.tibtech.2010.07.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Revised: 06/29/2010] [Accepted: 07/01/2010] [Indexed: 01/11/2023]
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24
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Harwich MD, Alves JM, Buck GA, Strauss JF, Patterson JL, Oki AT, Girerd PH, Jefferson KK. Drawing the line between commensal and pathogenic Gardnerella vaginalis through genome analysis and virulence studies. BMC Genomics 2010; 11:375. [PMID: 20540756 PMCID: PMC2890570 DOI: 10.1186/1471-2164-11-375] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 06/11/2010] [Indexed: 11/10/2022] Open
Abstract
Background Worldwide, bacterial vaginosis (BV) is the most common vaginal disorder. It is associated with risk for preterm birth and HIV infection. The etiology of the condition has been debated for nearly half a century and the lack of knowledge about its cause and progression has stymied efforts to improve therapy and prevention. Gardnerella vaginalis was originally identified as the causative agent, but subsequent findings that it is commonly isolated from seemingly healthy women cast doubt on this claim. Recent studies shedding light on the virulence properties of G. vaginalis, however, have drawn the species back into the spotlight. Results In this study, we sequenced the genomes of a strain of G. vaginalis from a healthy woman, and one from a woman with bacterial vaginosis. Comparative analysis of the genomes revealed significant divergence and in vitro studies indicated disparities in the virulence potential of the two strains. The commensal isolate exhibited reduced cytotoxicity and yet the cytolysin proteins encoded by the two strains were nearly identical, differing at a single amino acid, and were transcribed at similar levels. The BV-associated strain encoded a different variant of a biofilm associated protein gene and demonstrated greater adherence, aggregation, and biofilm formation. Using filters with different pore sizes, we found that direct contact between the bacteria and epithelial cells is required for cytotoxicity. Conclusions The results indicated that contact is required for cytotoxicity and suggested that reduced cytotoxicity in the commensal isolate could be due to impaired adherence. This study outlines two distinct genotypic variants of G. vaginalis, one apparently commensal and one pathogenic, and presents evidence for disparate virulence potentials.
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Affiliation(s)
- Michael D Harwich
- Department of Microbiology and Immunology, Medical College of Virginia Campus of Virginia Commonwealth University, Richmond, VA 23298, USA
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Hemmerich C, Buechlein A, Podicheti R, Revanna KV, Dong Q. An Ergatis-based prokaryotic genome annotation web server. ACTA ACUST UNITED AC 2010; 26:1122-4. [PMID: 20194626 DOI: 10.1093/bioinformatics/btq090] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SUMMARY Ergatis is a flexible workflow management system for designing and executing complex bioinformatics pipelines. However, its complexity restricts its usage to only highly skilled bioinformaticians. We have developed a web-based prokaryotic genome annotation server, Integrative Services for Genomics Analysis (ISGA), which builds upon the Ergatis workflow system, integrates other dynamic analysis tools and provides intuitive web interfaces for biologists to customize and execute their own annotation pipelines. ISGA is designed to be installed at genomics core facilities and be used directly by biologists. AVAILABILITY ISGA is accessible at http://isga.cgb.indiana.edu/ and the system is also freely available for local installation.
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Affiliation(s)
- Chris Hemmerich
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
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