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Alsmark, UCM
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Publications (10 of 16) Show all publications
Sikora, P., Andersson, S., Winiecka-Krusnell, J., Hallstrom, B., Alsmark, C., Troell, K., . . . Arrighi, R. B. G. (2017). Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes. Journal of Clinical Microbiology, 55(3), 844-858
Open this publication in new window or tab >>Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes
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2017 (English)In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 55, no 3, p. 844-858Article in journal (Refereed) Published
Abstract [en]

In order to improve genotyping and epidemiological analysis of Cryptosporidium spp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 different Cryptosporidium hominis patient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17X and 490X coverage. Sequence homologybased functional annotation identified several genes of interest, including the gene encoding Cryptosporidium oocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to the Cryptosporidium parvum reference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in the C. hominis tree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencing Cryptosporidium directly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes of Cryptosporidium from human fecal samples, while alluding to the potential for a higher degree of genotyping within Cryptosporidium epidemiology.

Place, publisher, year, edition, pages
AMER SOC MICROBIOLOGY, 2017
Keywords
cryptosporidiosis, immunomagnetic separation, clinical parasitology, genome sequencing
National Category
Microbiology
Identifiers
urn:nbn:se:uu:diva-320277 (URN)10.1128/JCM.01798-16 (DOI)000397595300022 ()28003424 (PubMedID)
Available from: 2017-04-28 Created: 2017-04-28 Last updated: 2017-04-28Bibliographically approved
Troell, K., Hallstrom, B., Divne, A.-M., Alsmark, C., Arrighi, R., Huss, M., . . . Bertilsson, S. (2016). Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes. BMC Genomics, 17, Article ID 471.
Open this publication in new window or tab >>Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes
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2016 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 17, article id 471Article in journal (Refereed) Published
Abstract [en]

Background: Infectious disease involving multiple genetically distinct populations of pathogens is frequently concurrent, but difficult to detect or describe with current routine methodology. Cryptosporidium sp. is a widespread gastrointestinal protozoan of global significance in both animals and humans. It cannot be easily maintained in culture and infections of multiple strains have been reported. To explore the potential use of single cell genomics methodology for revealing genome-level variation in clinical samples from Cryptosporidium-infected hosts, we sorted individual oocysts for subsequent genome amplification and full-genome sequencing. Results: Cells were identified with fluorescent antibodies with an 80 % success rate for the entire single cell genomics workflow, demonstrating that the methodology can be applied directly to purified fecal samples. Ten amplified genomes from sorted single cells were selected for genome sequencing and compared both to the original population and a reference genome in order to evaluate the accuracy and performance of the method. Single cell genome coverage was on average 81 % even with a moderate sequencing effort and by combining the 10 single cell genomes, the full genome was accounted for. By a comparison to the original sample, biological variation could be distinguished and separated from noise introduced in the amplification. Conclusions: As a proof of principle, we have demonstrated the power of applying single cell genomics to dissect infectious disease caused by closely related parasite species or subtypes. The workflow can easily be expanded and adapted to target other protozoans, and potential applications include mapping genome-encoded traits, virulence, pathogenicity, host specificity and resistance at the level of cells as truly meaningful biological units.

Keywords
Apicomplexa, Single cell genomics, Whole genome amplification, Cryptosporidium, Multiple infection, FACS
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
urn:nbn:se:uu:diva-299711 (URN)10.1186/s12864-016-2815-y (DOI)000378380600001 ()27338614 (PubMedID)
Funder
Swedish Civil Contingencies Agency, DNR2012-172 1109-2015-3.4.4Swedish Research Council, 2012-3892 2012-5095
Available from: 2016-07-26 Created: 2016-07-26 Last updated: 2017-11-28Bibliographically approved
Vikeved, E., Backlund, A. & Alsmark, C. (2016). The Dynamics of Lateral Gene Transfer in Genus Leishmania - A Route for Adaptation and Species Diversification. PLoS Neglected Tropical Diseases, 10(1), Article ID e0004326.
Open this publication in new window or tab >>The Dynamics of Lateral Gene Transfer in Genus Leishmania - A Route for Adaptation and Species Diversification
2016 (English)In: PLoS Neglected Tropical Diseases, ISSN 1935-2727, E-ISSN 1935-2735, Vol. 10, no 1, article id e0004326Article in journal (Refereed) Published
Abstract [en]

Background The genome of Leishmania major harbours a comparably high proportion of genes of prokaryote origin, acquired by lateral gene transfer (LGT). Some of these are present in closely related trypanosomatids, while some are detected in Leishmania only. We have evaluated the impact and destiny of LGT in genus Leishmania. Methodology/Principal Findings To study the dynamics and fate of LGTs we have performed phylogenetic, as well as nucleotide and amino acid composition analyses within orthologous groups of LGTs detected in Leishmania. A set of universal trypanosomatid LGTs was added as a reference group. Both groups of LGTs have, to some extent, ameliorated to resemble the recipient genomes. However, while virtually all of the universal trypanosomatid LGTs are distributed and conserved in the entire genus Leishmania, the LGTs uniquely present in genus Leishmania are more prone to gene loss and display faster rates of evolution. Furthermore, a PCR based approach has been employed to ascertain the presence of a set of twenty LGTs uniquely present in genus Leishmania, and three universal trypanosomatid LGTs, in ten additional strains of Leishmania. Evolutionary rates and predicted expression levels of these LGTs have also been estimated. Ten of the twenty LGTs are distributed and conserved in all species investigated, while the remainder have been subjected to modifications, or undergone pseudogenization, degradation or loss in one or more species. Conclusions/Significance LGTs unique to the genus Leishmania have been acquired after the divergence of Leishmania from the other trypanosomatids, and are evolving faster than their recipient genomes. This implies that LGT in genus Leishmania is a continuous and dynamic process contributing to species differentiation and speciation. This study also highlights the importance of carefully evaluating these dynamic genes, e.g. as LGTs have been suggested as potential drug targets.

National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-294607 (URN)10.1371/journal.pntd.0004326 (DOI)000372565700039 ()26730948 (PubMedID)
Funder
Swedish Research Council Formas, 2008-1366
Available from: 2016-05-26 Created: 2016-05-25 Last updated: 2018-12-05Bibliographically approved
Koptina, A., Strese, Å., Backlund, A. & Alsmark, C. (2015). Challenges to get axenic cultures of Trichomonas spp.: A new approach in eradication of contaminants and maintenance of laboratory microbiological cultures. Journal of Microbiological Methods, 118, 25-30
Open this publication in new window or tab >>Challenges to get axenic cultures of Trichomonas spp.: A new approach in eradication of contaminants and maintenance of laboratory microbiological cultures
2015 (English)In: Journal of Microbiological Methods, ISSN 0167-7012, E-ISSN 1872-8359, Vol. 118, p. 25-30Article in journal (Refereed) Published
Abstract [en]

Contamination of microbiological and cell cultures is a major problem in many scientific and clinical laboratories as well as bioproduct manufacturers worldwide. In the current study we established a rapid (9 day) method to detect and eliminate fungal and bacterial contamination in cultures of the unicellular eukaryote Trichomonas spp. The developed method combines identification of the contaminating microorganisms using PCR and sequencing of the 16/18S regions followed by phylogenetic analysis. The next step was a phylogeny-guided selection of antibiotic treatments. We then used a two-step propidium iodide-resorufin assay to test the effect of selected antibiotics. The result was a quick and worthwhile purification of trichomonad laboratory cultures. Our workflow may also be implemented to obtain new isolates of trichomonads from clinical samples if initial broad-spectrum antibiotic therapy fails.

Keywords
Trichomonas spp., Contamination, Resorufin, Propidium iodide, Antibiotic, Phylogeny
National Category
Pharmaceutical Sciences
Identifiers
urn:nbn:se:uu:diva-270634 (URN)10.1016/j.mimet.2015.08.009 (DOI)000364892300004 ()26284963 (PubMedID)
Funder
Carl Tryggers foundation , CTS KF15:6Swedish Research Council Formas, 2008-1366
Available from: 2016-01-01 Created: 2016-01-01 Last updated: 2018-01-10Bibliographically approved
Hirt, R. P., Alsmark, C. & Embley, T. M. (2015). Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites. Current Opinion in Microbiology, 23, 155-162
Open this publication in new window or tab >>Lateral gene transfers and the origins of the eukaryote proteome: a view from microbial parasites
2015 (English)In: Current Opinion in Microbiology, ISSN 1369-5274, E-ISSN 1879-0364, Vol. 23, p. 155-162Article, review/survey (Refereed) Published
Abstract [en]

Our knowledge of the extent and functional impact of lateral gene transfer (LGT) from prokaryotes to eukaryotes, outside of endosymbiosis, is still rather limited. Here we review the recent literature, focusing mainly on microbial parasites, indicating that LGT from diverse prokaryotes has played a significant role in the evolution of a number of lineages, and by extension throughout eukaryotic evolution. As might be expected, taxonomic biases for donor prokaryotes indicate that shared habitat is a major factor driving transfers. The LGTs identified predominantly affect enzymes from metabolic pathways, but over a third of LGT are genes for putative proteins of unknown function. Finally, we discuss the difficulties in analysing LOT among eukaryotes and suggest that high-throughput methodologies integrating different approaches are needed to achieve a more global understanding of the importance of LGT in eukaryotic evolution.

National Category
Microbiology in the medical area
Identifiers
urn:nbn:se:uu:diva-249056 (URN)10.1016/j.mib.2014.11.018 (DOI)000349879800024 ()
Available from: 2015-04-22 Created: 2015-04-10 Last updated: 2018-01-11Bibliographically approved
Strese, A., Backlund, A. & Alsmark, C. (2014). A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes. BMC Evolutionary Biology, 14, 119
Open this publication in new window or tab >>A recently transferred cluster of bacterial genes in Trichomonas vaginalis - lateral gene transfer and the fate of acquired genes
2014 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 14, p. 119-Article in journal (Refereed) Published
Abstract [en]

Background: Lateral Gene Transfer (LGT) has recently gained recognition as an important contributor to some eukaryote proteomes, but the mechanisms of acquisition and fixation in eukaryotic genomes are still uncertain. A previously defined norm for LGTs in microbial eukaryotes states that the majority are genes involved in metabolism, the LGTs are typically localized one by one, surrounded by vertically inherited genes on the chromosome, and phylogenetics shows that a broad collection of bacterial lineages have contributed to the transferome. Results: A unique 34 kbp long fragment with 27 clustered genes (TvLF) of prokaryote origin was identified in the sequenced genome of the protozoan parasite Trichomonas vaginalis. Using a PCR based approach we confirmed the presence of the orthologous fragment in four additional T. vaginalis strains. Detailed sequence analyses unambiguously suggest that TvLF is the result of one single, recent LGT event. The proposed donor is a close relative to the firmicute bacterium Peptoniphilus harei. High nucleotide sequence similarity between T. vaginalis strains, as well as to P. harei, and the absence of homologs in other Trichomonas species, suggests that the transfer event took place after the radiation of the genus Trichomonas. Some genes have undergone pseudogenization and degradation, indicating that they may not be retained in the future. Functional annotations reveal that genes involved in informational processes are particularly prone to degradation. Conclusions: We conclude that, although the majority of eukaryote LGTs are single gene occurrences, they may be acquired in clusters of several genes that are subsequently cleansed of evolutionarily less advantageous genes.

Keywords
Lateral gene transfer (LGT), Trichomonas, Peptoniphilus, Phylogeny
National Category
Evolutionary Biology Genetics Basic Medicine
Identifiers
urn:nbn:se:uu:diva-229452 (URN)10.1186/1471-2148-14-119 (DOI)000338382000001 ()
Available from: 2014-08-07 Created: 2014-08-07 Last updated: 2018-01-11Bibliographically approved
Koptina, A., Gunasekera, S., Muhammad, T., Bohlin, L., Alsmark, C. & Göransson, U. (2014). Microwave-assisted solid phase peptide synthesis of Asteropine A. In: Shabanov P.D. (Ed.), Phytopharm 2014, Saint-Petersburg, Russia 3-5 July 2014: . Paper presented at The 18th International Congress Phytopharm 2014, Saint-Petersburg, Russia 3-5 July 2014 (pp. 36). Saint-Petersburg, Russia, 12
Open this publication in new window or tab >>Microwave-assisted solid phase peptide synthesis of Asteropine A
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2014 (English)In: Phytopharm 2014, Saint-Petersburg, Russia 3-5 July 2014 / [ed] Shabanov P.D., Saint-Petersburg, Russia, 2014, Vol. 12, p. 36-Conference paper, Oral presentation with published abstract (Refereed)
Place, publisher, year, edition, pages
Saint-Petersburg, Russia: , 2014
Series
Onzory po kliniceskoj farmacologii i lekarstvennoj terapii, ISSN 1683-4100
National Category
Other Chemistry Topics
Research subject
Pharmacognosy
Identifiers
urn:nbn:se:uu:diva-245256 (URN)
Conference
The 18th International Congress Phytopharm 2014, Saint-Petersburg, Russia 3-5 July 2014
Funder
Carl Tryggers foundation EU, FP7, Seventh Framework Programme
Available from: 2015-02-26 Created: 2015-02-26 Last updated: 2015-03-04Bibliographically approved
Alsmark, C., Strese, Å., Wedén, C. & Backlund, A. (2013). Microbial diversity of Alcyonium digitatum. Phytochemistry Reviews, 12(3), 531-542
Open this publication in new window or tab >>Microbial diversity of Alcyonium digitatum
2013 (English)In: Phytochemistry Reviews, ISSN 1568-7767, E-ISSN 1572-980X, Vol. 12, no 3, p. 531-542Article, review/survey (Refereed) Published
Abstract [en]

Marine multi-cellular organisms are described as sources of many newly discovered bioactive compounds. Meanwhile, it has been demonstrated repeatedly for several natural products of reputed multicellular origin that they are, in fact, produced by endophytic unicellular organisms-such as microbial fungi or bacteria. Consequently, while studying compounds isolated from a living organism, it is essential to ensure that the sample integrity is not compromised. To test the diversity of the endobiome from Alcyonium digitatum, a cold water coral found along the Atlantic coasts of the northern hemisphere, we performed a culture dependent surveyed using a phylogenetic approach. A 1 cm(3) cube from the interior tissue of A. digitatum was excised under aseptic conditions, homogenized, spread onto agar-based growth medium plates and incubated in 22 A degrees C to promote microbial growth. Colonies were transferred to secondary medium plates, incubated, and after harvesting lysed using sterile water to release DNA. 16S and 23S rDNA regions were amplified using PCR, and sequenced for systematic evaluation using phylogenetic analysis. From this survey we identified a broad selection of bacteria, predominantly of the alpha-proteobacterial, bacteriodete, actinobacterial and firmicute lineages, demonstrating a significant biodiversity of the coral bacterial endobiome.

Keywords
Alcyonium digitatum, Microbial endobiome, Phylogeny, Biodiversity
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-211142 (URN)10.1007/s11101-012-9229-5 (DOI)000324653400013 ()
Available from: 2013-11-20 Created: 2013-11-20 Last updated: 2017-12-06Bibliographically approved
Alsmark, C., Foster, P. G., Sicheritz-Ponten, T., Nakjang, S., Embley, T. M. & Hirt, R. P. (2013). Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. Genome Biology, 14(2), R19
Open this publication in new window or tab >>Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes
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2013 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, no 2, p. R19-Article in journal (Refereed) Published
Abstract [en]

Background: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution. Results: We used a phylogenomic approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers, dramatically affecting the enzymes of core pathways, particularly amino acid and sugar metabolism, but also providing new genes of potential adaptive significance in the life of parasites. A broad range of prokaryotic donors is involved in such transfers, but there is clear and significant enrichment for bacterial groups that share the same habitats, including the human microbiota, as the parasites investigated. Conclusions: Our data show that ecology and lifestyle strongly influence gene origins and opportunities for gene transfer and reveal that, although the outlines of the core eukaryotic metabolism are conserved among lineages, the genes making up those pathways can have very different origins in different eukaryotes. Thus, from the perspective of the effects of lateral gene transfer on individual gene ancestries in different lineages, eukaryotic metabolism appears to be chimeric.

Keywords
Genome evolution, phylogenomics, lateral gene transfer, eukaryotes, parasites
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-206676 (URN)10.1186/gb-2013-14-2-r19 (DOI)000322388800009 ()
Available from: 2013-09-03 Created: 2013-09-02 Last updated: 2017-12-06Bibliographically approved
Bohlin, L., Alsmark, C., Göransson, U., Klum, M., Weden, C. & Backlund, A. (2012). Strategies and methods for a sustainable search for bioactive compounds. Paper presented at International Congress on Natural Products Research on Global Change, Natural Products and Human Health/8th Joint Meeting of AFERP, ASP, GA, PSE and SIF, JUL 28-AUG 01, 2012, New York, NY. Planta Medica, 78(11), 1031-1032
Open this publication in new window or tab >>Strategies and methods for a sustainable search for bioactive compounds
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2012 (English)In: Planta Medica, ISSN 0032-0943, E-ISSN 1439-0221, Vol. 78, no 11, p. 1031-1032Article in journal, Meeting abstract (Other academic) Published
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-181205 (URN)10.1055/s-0032-1320200 (DOI)000307042800015 ()
Conference
International Congress on Natural Products Research on Global Change, Natural Products and Human Health/8th Joint Meeting of AFERP, ASP, GA, PSE and SIF, JUL 28-AUG 01, 2012, New York, NY
Available from: 2012-09-24 Created: 2012-09-19 Last updated: 2017-12-07Bibliographically approved
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