Robust sampling and preservation of DNA for microbial community profiling in field experiments View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2019-12

AUTHORS

Anneloes E. Groenenboom, Eddy J. Smid, Sijmen E. Schoustra

ABSTRACT

OBJECTIVE: Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product. RESULTS: Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas. More... »

PAGES

159

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s13104-019-4187-2

DOI

http://dx.doi.org/10.1186/s13104-019-4187-2

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1112945185

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/30902062


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Wageningen University & Research", 
          "id": "https://www.grid.ac/institutes/grid.4818.5", 
          "name": [
            "Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands", 
            "Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Groenenboom", 
        "givenName": "Anneloes E.", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Wageningen University & Research", 
          "id": "https://www.grid.ac/institutes/grid.4818.5", 
          "name": [
            "Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Smid", 
        "givenName": "Eddy J.", 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Zambia", 
          "id": "https://www.grid.ac/institutes/grid.12984.36", 
          "name": [
            "Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands", 
            "Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka, Zambia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schoustra", 
        "givenName": "Sijmen E.", 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1128/aem.71.11.6702-6710.2005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005272250"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.lwt.2004.05.008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1008944919"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.f.303", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009032055", 
          "https://doi.org/10.1038/nmeth.f.303"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.f.303", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009032055", 
          "https://doi.org/10.1038/nmeth.f.303"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/1574-6941.12008", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1015908633"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1472-6785-4-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017297341", 
          "https://doi.org/10.1186/1472-6785-4-4"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1590/1678-775720130683", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1026267504"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10295-008-0393-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028126297", 
          "https://doi.org/10.1007/s10295-008-0393-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1007/s10295-008-0393-y", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028126297", 
          "https://doi.org/10.1007/s10295-008-0393-y"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.fsigss.2009.08.126", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028722816"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1078/0723-2020-00076", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033340792"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0063948", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037018603"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1167/iovs.09-3737", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042412984"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.mimet.2006.05.010", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1048633840"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1128/msphere.00226-16", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062727555"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2019-12", 
    "datePublishedReg": "2019-12-01", 
    "description": "OBJECTIVE: Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product.\nRESULTS: Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/s13104-019-4187-2", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1039457", 
        "issn": [
          "1756-0500"
        ], 
        "name": "BMC Research Notes", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "12"
      }
    ], 
    "name": "Robust sampling and preservation of DNA for microbial community profiling in field experiments", 
    "pagination": "159", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "7088982eafd54e7705fead3173a260875f10f798c73c106ac973c31ec05946e7"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "30902062"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "101462768"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/s13104-019-4187-2"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1112945185"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/s13104-019-4187-2", 
      "https://app.dimensions.ai/details/publication/pub.1112945185"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T14:18", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000372_0000000372/records_117106_00000003.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "https://link.springer.com/10.1186%2Fs13104-019-4187-2"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13104-019-4187-2'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13104-019-4187-2'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13104-019-4187-2'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13104-019-4187-2'


 

This table displays all metadata directly associated to this object as RDF triples.

126 TRIPLES      21 PREDICATES      42 URIs      21 LITERALS      9 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/s13104-019-4187-2 schema:about anzsrc-for:06
2 anzsrc-for:0605
3 schema:author N9a4c41002397438686f9b97bb00274f7
4 schema:citation sg:pub.10.1007/s10295-008-0393-y
5 sg:pub.10.1038/nmeth.f.303
6 sg:pub.10.1186/1472-6785-4-4
7 https://doi.org/10.1016/j.fsigss.2009.08.126
8 https://doi.org/10.1016/j.lwt.2004.05.008
9 https://doi.org/10.1016/j.mimet.2006.05.010
10 https://doi.org/10.1078/0723-2020-00076
11 https://doi.org/10.1111/1574-6941.12008
12 https://doi.org/10.1128/aem.71.11.6702-6710.2005
13 https://doi.org/10.1128/msphere.00226-16
14 https://doi.org/10.1167/iovs.09-3737
15 https://doi.org/10.1371/journal.pone.0063948
16 https://doi.org/10.1590/1678-775720130683
17 schema:datePublished 2019-12
18 schema:datePublishedReg 2019-12-01
19 schema:description OBJECTIVE: Stabilising samples of microbial communities for DNA extraction without access to laboratory equipment can be a challenging task. In this paper we propose a method using filter paper disks for the preservation of DNA from diverse microbial communities which are found in a fermented milk product. RESULTS: Small adaptations to the DNA extraction method used for liquid fermented milk delivered DNA of sufficient amounts and quality to be used for later analyses, e.g. full community 16S amplicon sequencing. The microbial community structure obtained via the filter paper method showed sufficient resemblance to the structure obtain via the traditional DNA extraction from the liquid milk sample. This method can therefore successfully be used to analyse diverse microbial communities from fermented milk products from remote areas.
20 schema:genre research_article
21 schema:inLanguage en
22 schema:isAccessibleForFree true
23 schema:isPartOf N3e2790adb15c4ff9aaad25643231d92e
24 Nd63bfe7e580e424ba65b2fbd7e93e006
25 sg:journal.1039457
26 schema:name Robust sampling and preservation of DNA for microbial community profiling in field experiments
27 schema:pagination 159
28 schema:productId N04051a3484d148aebb050f3d4bcdfd57
29 N3aeed4e880a9459ba0ae5e65d7bcae8c
30 Nc91cd19068414193856174bce810e860
31 Nc9d1695fcb73458a942d15e60777f0f7
32 Nfbb5c209063045199830eab388e55939
33 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112945185
34 https://doi.org/10.1186/s13104-019-4187-2
35 schema:sdDatePublished 2019-04-11T14:18
36 schema:sdLicense https://scigraph.springernature.com/explorer/license/
37 schema:sdPublisher Nd22736b33ad042bc8cb49a8a6aece31a
38 schema:url https://link.springer.com/10.1186%2Fs13104-019-4187-2
39 sgo:license sg:explorer/license/
40 sgo:sdDataset articles
41 rdf:type schema:ScholarlyArticle
42 N04051a3484d148aebb050f3d4bcdfd57 schema:name pubmed_id
43 schema:value 30902062
44 rdf:type schema:PropertyValue
45 N1a12eedf9685497da51c00e631d20edb schema:affiliation https://www.grid.ac/institutes/grid.4818.5
46 schema:familyName Groenenboom
47 schema:givenName Anneloes E.
48 rdf:type schema:Person
49 N3aeed4e880a9459ba0ae5e65d7bcae8c schema:name dimensions_id
50 schema:value pub.1112945185
51 rdf:type schema:PropertyValue
52 N3e2790adb15c4ff9aaad25643231d92e schema:volumeNumber 12
53 rdf:type schema:PublicationVolume
54 N66afe55cb74944aa8deae747004d076b rdf:first N78ccc4adc6284a4b95fe2f15d83dbf4b
55 rdf:rest Nf118c0ca1e36412d976744633de6b8eb
56 N78ccc4adc6284a4b95fe2f15d83dbf4b schema:affiliation https://www.grid.ac/institutes/grid.4818.5
57 schema:familyName Smid
58 schema:givenName Eddy J.
59 rdf:type schema:Person
60 N9a4c41002397438686f9b97bb00274f7 rdf:first N1a12eedf9685497da51c00e631d20edb
61 rdf:rest N66afe55cb74944aa8deae747004d076b
62 Nb73c814799c143198096de36a62c664d schema:affiliation https://www.grid.ac/institutes/grid.12984.36
63 schema:familyName Schoustra
64 schema:givenName Sijmen E.
65 rdf:type schema:Person
66 Nc91cd19068414193856174bce810e860 schema:name doi
67 schema:value 10.1186/s13104-019-4187-2
68 rdf:type schema:PropertyValue
69 Nc9d1695fcb73458a942d15e60777f0f7 schema:name nlm_unique_id
70 schema:value 101462768
71 rdf:type schema:PropertyValue
72 Nd22736b33ad042bc8cb49a8a6aece31a schema:name Springer Nature - SN SciGraph project
73 rdf:type schema:Organization
74 Nd63bfe7e580e424ba65b2fbd7e93e006 schema:issueNumber 1
75 rdf:type schema:PublicationIssue
76 Nf118c0ca1e36412d976744633de6b8eb rdf:first Nb73c814799c143198096de36a62c664d
77 rdf:rest rdf:nil
78 Nfbb5c209063045199830eab388e55939 schema:name readcube_id
79 schema:value 7088982eafd54e7705fead3173a260875f10f798c73c106ac973c31ec05946e7
80 rdf:type schema:PropertyValue
81 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
82 schema:name Biological Sciences
83 rdf:type schema:DefinedTerm
84 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
85 schema:name Microbiology
86 rdf:type schema:DefinedTerm
87 sg:journal.1039457 schema:issn 1756-0500
88 schema:name BMC Research Notes
89 rdf:type schema:Periodical
90 sg:pub.10.1007/s10295-008-0393-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1028126297
91 https://doi.org/10.1007/s10295-008-0393-y
92 rdf:type schema:CreativeWork
93 sg:pub.10.1038/nmeth.f.303 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009032055
94 https://doi.org/10.1038/nmeth.f.303
95 rdf:type schema:CreativeWork
96 sg:pub.10.1186/1472-6785-4-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017297341
97 https://doi.org/10.1186/1472-6785-4-4
98 rdf:type schema:CreativeWork
99 https://doi.org/10.1016/j.fsigss.2009.08.126 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028722816
100 rdf:type schema:CreativeWork
101 https://doi.org/10.1016/j.lwt.2004.05.008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008944919
102 rdf:type schema:CreativeWork
103 https://doi.org/10.1016/j.mimet.2006.05.010 schema:sameAs https://app.dimensions.ai/details/publication/pub.1048633840
104 rdf:type schema:CreativeWork
105 https://doi.org/10.1078/0723-2020-00076 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033340792
106 rdf:type schema:CreativeWork
107 https://doi.org/10.1111/1574-6941.12008 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015908633
108 rdf:type schema:CreativeWork
109 https://doi.org/10.1128/aem.71.11.6702-6710.2005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005272250
110 rdf:type schema:CreativeWork
111 https://doi.org/10.1128/msphere.00226-16 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062727555
112 rdf:type schema:CreativeWork
113 https://doi.org/10.1167/iovs.09-3737 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042412984
114 rdf:type schema:CreativeWork
115 https://doi.org/10.1371/journal.pone.0063948 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037018603
116 rdf:type schema:CreativeWork
117 https://doi.org/10.1590/1678-775720130683 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026267504
118 rdf:type schema:CreativeWork
119 https://www.grid.ac/institutes/grid.12984.36 schema:alternateName University of Zambia
120 schema:name Department of Food Science and Nutrition, School of Agricultural Sciences, University of Zambia, Lusaka, Zambia
121 Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
122 rdf:type schema:Organization
123 https://www.grid.ac/institutes/grid.4818.5 schema:alternateName Wageningen University & Research
124 schema:name Laboratory of Food Microbiology, Wageningen University and Research, Wageningen, The Netherlands
125 Laboratory of Genetics, Wageningen University and Research, Wageningen, The Netherlands
126 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...