Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity
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{"title"=>"Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity", "type"=>"journal", "authors"=>[{"first_name"=>"Frederiek Maarten", "last_name"=>"Kerckhof", "scopus_author_id"=>"55251633600"}, {"first_name"=>"Emilie N P", "last_name"=>"Courtens", "scopus_author_id"=>"55251677600"}, {"first_name"=>"Annelies", "last_name"=>"Geirnaert", "scopus_author_id"=>"55251712600"}, {"first_name"=>"Sven", "last_name"=>"Hoefman", "scopus_author_id"=>"36117962100"}, {"first_name"=>"Adrian", "last_name"=>"Ho", "scopus_author_id"=>"48661295600"}, {"first_name"=>"Ramiro", "last_name"=>"Vilchez-Vargas", "scopus_author_id"=>"35491935800"}, {"first_name"=>"Dietmar H.", "last_name"=>"Pieper", "scopus_author_id"=>"7005929271"}, {"first_name"=>"Ruy", "last_name"=>"Jauregui", "scopus_author_id"=>"16052509900"}, {"first_name"=>"Siegfried E.", "last_name"=>"Vlaeminck", "scopus_author_id"=>"16246728200"}, {"first_name"=>"Tom", "last_name"=>"Van De Wiele", "scopus_author_id"=>"6602834915"}, {"first_name"=>"Peter", "last_name"=>"Vandamme", "scopus_author_id"=>"56211244100"}, {"first_name"=>"Kim", "last_name"=>"Heylen", "scopus_author_id"=>"8934856800"}, {"first_name"=>"Nico", "last_name"=>"Boon", "scopus_author_id"=>"7005091577"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84903281208", "sgr"=>"84903281208", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0099517", "pmid"=>"24937032", "isbn"=>"1932-6203 (Electronic)\r1932-6203 (Linking)", "pui"=>"373396670"}, "id"=>"50138961-6884-31cb-9dd2-74c5721130ce", "abstract"=>"The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at -80 °C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. 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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1537695"], "description"=>"<p>Error bars represent error-propagated standard errors A) the MOB community on NMS and dNMS cultivation medium. The activity recovery was the percentage of specific MOR (mmol CH<sub>4 </sub>g<sup>−1</sup> VS d<sup>−1</sup>) from the pre-freezing activity test (t<sub>0</sub> to t<sub>1</sub>) that was obtained in each experimental condition in the post-freezing activity test (t<sub>2</sub> to t<sub>3</sub>) B) The different functional members in the OLAND community. The activity recovery was the percentage of specific activity (mg N g<sup>−1</sup> VSS d<sup>−1</sup>) for either aerobic or anaerobic ammonium oxidation (AOB and AnAOB) or nitrite oxidation (NOB), from the pre-freezing activity test (t<sub>0</sub> to t<sub>1</sub>) that was obtained in each experimental condition in the post-freezing activity test (t<sub>2</sub> to t<sub>3</sub>) C) short chain fatty acid production by the fecal microbiome. The activity recovery was the percentage of SCFA produced in the pre-freezing activity test (t<sub>0</sub> to t<sub>1</sub>) that was obtained in each experimental condition in the post-freezing activity test (t<sub>2</sub> to t<sub>3</sub>). Total SCFA, acetate, propionate and butyrate were measured.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Environmental biotechnology", "Cryobiology", "ecology", "Community Ecology", "community structure", "microbial ecology", "microbiology", "Species interactions"], "article_id"=>1059815, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frederiek-Maarten Kerckhof", "Emilie N. P. Courtens", "Annelies Geirnaert", "Sven Hoefman", "Adrian Ho", "Ramiro Vilchez-Vargas", "Dietmar H. Pieper", "Ruy Jauregui", "Siegfried E. Vlaeminck", "Tom Van de Wiele", "Peter Vandamme", "Kim Heylen", "Nico Boon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099517.g002", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Functionality_recovery_after_cryopreservation_/1059815", "title"=>"Functionality recovery after cryopreservation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537801", "https://ndownloader.figshare.com/files/1537802", "https://ndownloader.figshare.com/files/1537803", "https://ndownloader.figshare.com/files/1537804", "https://ndownloader.figshare.com/files/1537805", "https://ndownloader.figshare.com/files/1537806", "https://ndownloader.figshare.com/files/1537807", "https://ndownloader.figshare.com/files/1537808", "https://ndownloader.figshare.com/files/1537810", "https://ndownloader.figshare.com/files/1537811", "https://ndownloader.figshare.com/files/1537812", "https://ndownloader.figshare.com/files/1537813", "https://ndownloader.figshare.com/files/1537814", "https://ndownloader.figshare.com/files/1537815", "https://ndownloader.figshare.com/files/1537817"], "description"=>"<div><p>The use of mixed microbial communities (microbiomes) for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA). Microbiomes were selected based upon relevance towards applications: (1) a methanotrophic co-culture (MOB), with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2) an oxygen limited autotrophic nitrification/denitrification (OLAND) biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3) fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at −80°C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB) and anaerobic AOB (AnAOB, anammox) in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO) and DMSO plus trehalose and tryptic soy broth (DMSO+TT)] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing) was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.</p></div>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Environmental biotechnology", "Cryobiology", "ecology", "Community Ecology", "community structure", "microbial ecology", "microbiology", "Species interactions", "cryopreservation", "microbial", "communities", "conserved", "functionality"], "article_id"=>1059912, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frederiek-Maarten Kerckhof", "Emilie N. P. Courtens", "Annelies Geirnaert", "Sven Hoefman", "Adrian Ho", "Ramiro Vilchez-Vargas", "Dietmar H. Pieper", "Ruy Jauregui", "Siegfried E. Vlaeminck", "Tom Van de Wiele", "Peter Vandamme", "Kim Heylen", "Nico Boon"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0099517.s001", "https://dx.doi.org/10.1371/journal.pone.0099517.s002", "https://dx.doi.org/10.1371/journal.pone.0099517.s003", "https://dx.doi.org/10.1371/journal.pone.0099517.s004", "https://dx.doi.org/10.1371/journal.pone.0099517.s005", "https://dx.doi.org/10.1371/journal.pone.0099517.s006", "https://dx.doi.org/10.1371/journal.pone.0099517.s007", "https://dx.doi.org/10.1371/journal.pone.0099517.s008", "https://dx.doi.org/10.1371/journal.pone.0099517.s009", "https://dx.doi.org/10.1371/journal.pone.0099517.s010", "https://dx.doi.org/10.1371/journal.pone.0099517.s011", "https://dx.doi.org/10.1371/journal.pone.0099517.s012", "https://dx.doi.org/10.1371/journal.pone.0099517.s013", "https://dx.doi.org/10.1371/journal.pone.0099517.s014", "https://dx.doi.org/10.1371/journal.pone.0099517.s015"], "stats"=>{"downloads"=>18, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Optimized_Cryopreservation_of_Mixed_Microbial_Communities_for_Conserved_Functionality_and_Diversity_/1059912", "title"=>"Optimized Cryopreservation of Mixed Microbial Communities for Conserved Functionality and Diversity", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-06-17 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537780"], "description"=>"<p>Cryoprotective agents (CPA) used in the crypreservation design.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Environmental biotechnology", "Cryobiology", "ecology", "Community Ecology", "community structure", "microbial ecology", "microbiology", "Species interactions", "agents", "crypreservation"], "article_id"=>1059895, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frederiek-Maarten Kerckhof", "Emilie N. P. Courtens", "Annelies Geirnaert", "Sven Hoefman", "Adrian Ho", "Ramiro Vilchez-Vargas", "Dietmar H. Pieper", "Ruy Jauregui", "Siegfried E. Vlaeminck", "Tom Van de Wiele", "Peter Vandamme", "Kim Heylen", "Nico Boon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099517.t001", "stats"=>{"downloads"=>4, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cryoprotective_agents_CPA_used_in_the_crypreservation_design_/1059895", "title"=>"Cryoprotective agents (CPA) used in the crypreservation design.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-06-17 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537726"], "description"=>"<p>The distances are displayed for MOB biomass cultivated on NMS (A), dNMS (C), OLAND biomass (B) and fecal biomass (D). The reference represents the distance between t<sub>0</sub> and t<sub>1</sub> whilst the other bars represent the distance between t<sub>0</sub> and the several conditions at t<sub>3</sub>. Error bars (for MOB and fecal samples) represent standard deviations (n = 4 in A, n = 6 for reference in C and 4 for the other means, n = 4 in D). No reference is available for the OLAND biomass because time point t<sub>1</sub> was not assessed using Illumina.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Environmental biotechnology", "Cryobiology", "ecology", "Community Ecology", "community structure", "microbial ecology", "microbiology", "Species interactions", "abundance-based", "jaccard", "distances", "stages"], "article_id"=>1059845, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frederiek-Maarten Kerckhof", "Emilie N. P. Courtens", "Annelies Geirnaert", "Sven Hoefman", "Adrian Ho", "Ramiro Vilchez-Vargas", "Dietmar H. Pieper", "Ruy Jauregui", "Siegfried E. Vlaeminck", "Tom Van de Wiele", "Peter Vandamme", "Kim Heylen", "Nico Boon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099517.g006", "stats"=>{"downloads"=>4, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_abundance_based_Jaccard_Ru_382_i_269_ka_distances_between_experimental_stages_and_conditions_/1059845", "title"=>"Average abundance-based Jaccard (Ružička) distances between experimental stages and conditions.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537762"], "description"=>"<p>Sequences were aligned using the mothur implementation of the NAST algorithm with the Silva v102 reference alignment. RAxML was used to construct an extended majority rule bootstrap consensus tree with the GTR + GAMMA substitution model and 1000 bootstrap iterations. This bootstrap consensus tree was visualized using iTol. The colored bars represent log transformed absolute abundances with the log transformation as suggested by Anderson and colleagues <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099517#pone.0099517-Anderson1\" target=\"_blank\">[74]</a> with base 10. Before transformation the samples were rarefied to the lowest sequence count. Black arrows point out OTUs that have a differential presence among experimental conditions. Classification was done based upon the Greengenes taxonomy (adapted to mothur from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099517#pone.0099517-Werner1\" target=\"_blank\">[53]</a>) with the naïve Bayesian classifier implemented in mothur (Wang algorithm).</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Environmental biotechnology", "Cryobiology", "ecology", "Community Ecology", "community structure", "microbial ecology", "microbiology", "Species interactions", "otu", "sequences", "oland"], "article_id"=>1059877, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frederiek-Maarten Kerckhof", "Emilie N. P. Courtens", "Annelies Geirnaert", "Sven Hoefman", "Adrian Ho", "Ramiro Vilchez-Vargas", "Dietmar H. Pieper", "Ruy Jauregui", "Siegfried E. Vlaeminck", "Tom Van de Wiele", "Peter Vandamme", "Kim Heylen", "Nico Boon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099517.g004", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_OTU_consensus_sequences_in_the_OLAND_samples_/1059877", "title"=>"Phylogenetic tree of OTU consensus sequences in the OLAND samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537779"], "description"=>"<p>Sequences were aligned using the mothur implementation of the NAST algorithm with the Silva v102 reference alignment. RAxML was used to construct an extended majority rule bootstrap consensus tree with the GTR + GAMMA substitution model and 1000 bootstrap iterations. This bootstrap consensus tree was visualized using iTol. The colored bars represent treatment-wise means (n = 2 except for fecal inoculum n = 1) of the log transformed absolute abundances with the log transformation as suggested by Anderson and colleagues <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099517#pone.0099517-Anderson1\" target=\"_blank\">[74]</a> with base 10. Before transformation the samples were rarefied to the lowest sequence count. Classification was done based upon the Greengenes taxonomy (adapted to mothur from <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0099517#pone.0099517-Werner1\" target=\"_blank\">[53]</a>) with the naïve Bayesian classifier implemented in mothur (Wang algorithm). Black arrows indicate OTUs with differential abundance among the experimental conditions.</p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Environmental biotechnology", "Cryobiology", "ecology", "Community Ecology", "community structure", "microbial ecology", "microbiology", "Species interactions", "otu", "sequences", "fecal"], "article_id"=>1059894, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frederiek-Maarten Kerckhof", "Emilie N. P. Courtens", "Annelies Geirnaert", "Sven Hoefman", "Adrian Ho", "Ramiro Vilchez-Vargas", "Dietmar H. Pieper", "Ruy Jauregui", "Siegfried E. Vlaeminck", "Tom Van de Wiele", "Peter Vandamme", "Kim Heylen", "Nico Boon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099517.g005", "stats"=>{"downloads"=>2, "page_views"=>61, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogenetic_tree_of_OTU_consensus_sequences_in_the_fecal_material_samples_/1059894", "title"=>"Phylogenetic tree of OTU consensus sequences in the fecal material samples.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:06:07"}
  • {"files"=>["https://ndownloader.figshare.com/files/1537688"], "description"=>"<p>The time is shown in days. In red the activity tests are shown. The freezing and thawing are shown in dark grey. DNA sampling was executed at t<sub>0</sub>, t<sub>1</sub> and t<sub>3.</sub></p>", "links"=>[], "tags"=>["biotechnology", "Applied microbiology", "Environmental biotechnology", "Cryobiology", "ecology", "Community Ecology", "community structure", "microbial ecology", "microbiology", "Species interactions", "sampling", "cryopreservation"], "article_id"=>1059807, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Frederiek-Maarten Kerckhof", "Emilie N. P. Courtens", "Annelies Geirnaert", "Sven Hoefman", "Adrian Ho", "Ramiro Vilchez-Vargas", "Dietmar H. Pieper", "Ruy Jauregui", "Siegfried E. Vlaeminck", "Tom Van de Wiele", "Peter Vandamme", "Kim Heylen", "Nico Boon"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0099517.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Timeline_and_sampling_strategy_of_the_cryopreservation_setup_/1059807", "title"=>"Timeline and sampling strategy of the cryopreservation setup.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-06-17 03:06:07"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[320]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[313]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[262]}]}
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