From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding Article Swipe
Małgorzata Chwalińska
,
Michał Karlicki
,
Sarah Romac
,
Fabrice Not
,
Anna Karnkowska
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3897/mbmg.9.163750
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.3897/mbmg.9.163750
In the last decades, environmental metabarcoding has revolutionised biodiversity research, particularly for microbial organisms such as protists, enabling large-scale assessments of diversity and ecological patterns across time and space. With the advent of long-read sequencing, Nanopore-based metabarcoding represents a promising alternative to short-read approaches. Due to the limited number of available studies, the effectiveness of Nanopore sequencing - alone or in combination with short-read data - for assessing the biodiversity and ecological patterns of protists in different ecosystems is not yet sufficiently explored. Here, we present BaNaNA (Barcoding Nanopore Neat Annotator), a pipeline designed to generate high-quality OTUs and abundance estimates from Nanopore sequencing data. The performance of the pipeline was evaluated using a mock community as well as on marine and freshwater environmental samples to demonstrate its relevance for protist biodiversity and ecological studies. Our results show that BaNaNA generates high-quality full-length 18S rDNAOTUs from Nanopore long reads that are directly comparable to short-read V4-18S rDNAASVs, supporting their synergistic use in long-term biodiversity studies. While both approaches reveal similar overall community diversity, long-read OTUs provide greater taxonomic resolution, richer phylogenetic information enabling the discovery of new clades and yield fewer false positives. These advantages make long-read Nanopore metabarcoding not only a powerful cost effective complement, but also a reliable replacement to short-read methods. By providing a pipeline for processing Nanopore data, BaNaNA paves the way for a broader application of long-read Nanopore sequencing in protist ecology and biodiversity research.
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From short to long reads: enhanced protist diversity profiling via Nanopore metabarcodingWork title
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2025Year of publication
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2025-10-08Full publication date if available
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Małgorzata Chwalińska, Michał Karlicki, Sarah Romac, Fabrice Not, Anna KarnkowskaList of authors in order
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https://doi.org/10.3897/mbmg.9.163750Publisher landing page
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goldOpen access status per OpenAlex
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0Total citation count in OpenAlex
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| abstract_inverted_index.mock | 114 |
| abstract_inverted_index.only | 200 |
| abstract_inverted_index.show | 137 |
| abstract_inverted_index.such | 14 |
| abstract_inverted_index.that | 138, 149 |
| abstract_inverted_index.time | 26 |
| abstract_inverted_index.well | 117 |
| abstract_inverted_index.with | 62 |
| abstract_inverted_index.Here, | 83 |
| abstract_inverted_index.These | 193 |
| abstract_inverted_index.While | 165 |
| abstract_inverted_index.alone | 58 |
| abstract_inverted_index.data, | 221 |
| abstract_inverted_index.data. | 104 |
| abstract_inverted_index.false | 191 |
| abstract_inverted_index.fewer | 190 |
| abstract_inverted_index.paves | 223 |
| abstract_inverted_index.reads | 148 |
| abstract_inverted_index.their | 158 |
| abstract_inverted_index.using | 112 |
| abstract_inverted_index.yield | 189 |
| abstract_inverted_index.BaNaNA | 86, 139, 222 |
| abstract_inverted_index.V4-18S | 155 |
| abstract_inverted_index.across | 25 |
| abstract_inverted_index.advent | 31 |
| abstract_inverted_index.clades | 187 |
| abstract_inverted_index.marine | 120 |
| abstract_inverted_index.number | 48 |
| abstract_inverted_index.reveal | 168 |
| abstract_inverted_index.richer | 179 |
| abstract_inverted_index.space. | 28 |
| abstract_inverted_index.broader | 228 |
| abstract_inverted_index.ecology | 236 |
| abstract_inverted_index.greater | 176 |
| abstract_inverted_index.limited | 47 |
| abstract_inverted_index.overall | 170 |
| abstract_inverted_index.present | 85 |
| abstract_inverted_index.protist | 130, 235 |
| abstract_inverted_index.provide | 175 |
| abstract_inverted_index.results | 136 |
| abstract_inverted_index.samples | 124 |
| abstract_inverted_index.similar | 169 |
| abstract_inverted_index.Nanopore | 55, 88, 102, 146, 197, 220, 232 |
| abstract_inverted_index.decades, | 3 |
| abstract_inverted_index.designed | 93 |
| abstract_inverted_index.directly | 151 |
| abstract_inverted_index.enabling | 17, 182 |
| abstract_inverted_index.generate | 95 |
| abstract_inverted_index.methods. | 213 |
| abstract_inverted_index.patterns | 24, 72 |
| abstract_inverted_index.pipeline | 92, 109, 217 |
| abstract_inverted_index.powerful | 202 |
| abstract_inverted_index.protists | 74 |
| abstract_inverted_index.rDNAOTUs | 144 |
| abstract_inverted_index.reliable | 209 |
| abstract_inverted_index.studies, | 51 |
| abstract_inverted_index.studies. | 134, 164 |
| abstract_inverted_index.abundance | 99 |
| abstract_inverted_index.assessing | 67 |
| abstract_inverted_index.available | 50 |
| abstract_inverted_index.community | 115, 171 |
| abstract_inverted_index.different | 76 |
| abstract_inverted_index.discovery | 184 |
| abstract_inverted_index.diversity | 21 |
| abstract_inverted_index.effective | 204 |
| abstract_inverted_index.estimates | 100 |
| abstract_inverted_index.evaluated | 111 |
| abstract_inverted_index.explored. | 82 |
| abstract_inverted_index.generates | 140 |
| abstract_inverted_index.long-read | 33, 173, 196, 231 |
| abstract_inverted_index.long-term | 162 |
| abstract_inverted_index.microbial | 12 |
| abstract_inverted_index.organisms | 13 |
| abstract_inverted_index.promising | 39 |
| abstract_inverted_index.protists, | 16 |
| abstract_inverted_index.providing | 215 |
| abstract_inverted_index.rDNAASVs, | 156 |
| abstract_inverted_index.relevance | 128 |
| abstract_inverted_index.research, | 9 |
| abstract_inverted_index.research. | 239 |
| abstract_inverted_index.taxonomic | 177 |
| abstract_inverted_index.(Barcoding | 87 |
| abstract_inverted_index.advantages | 194 |
| abstract_inverted_index.approaches | 167 |
| abstract_inverted_index.comparable | 152 |
| abstract_inverted_index.diversity, | 172 |
| abstract_inverted_index.ecological | 23, 71, 133 |
| abstract_inverted_index.ecosystems | 77 |
| abstract_inverted_index.freshwater | 122 |
| abstract_inverted_index.positives. | 192 |
| abstract_inverted_index.processing | 219 |
| abstract_inverted_index.represents | 37 |
| abstract_inverted_index.sequencing | 56, 103, 233 |
| abstract_inverted_index.short-read | 42, 63, 154, 212 |
| abstract_inverted_index.supporting | 157 |
| abstract_inverted_index.Annotator), | 90 |
| abstract_inverted_index.alternative | 40 |
| abstract_inverted_index.application | 229 |
| abstract_inverted_index.approaches. | 43 |
| abstract_inverted_index.assessments | 19 |
| abstract_inverted_index.combination | 61 |
| abstract_inverted_index.complement, | 205 |
| abstract_inverted_index.demonstrate | 126 |
| abstract_inverted_index.full-length | 142 |
| abstract_inverted_index.information | 181 |
| abstract_inverted_index.large-scale | 18 |
| abstract_inverted_index.performance | 106 |
| abstract_inverted_index.replacement | 210 |
| abstract_inverted_index.resolution, | 178 |
| abstract_inverted_index.sequencing, | 34 |
| abstract_inverted_index.synergistic | 159 |
| abstract_inverted_index.biodiversity | 8, 69, 131, 163, 238 |
| abstract_inverted_index.high-quality | 96, 141 |
| abstract_inverted_index.particularly | 10 |
| abstract_inverted_index.phylogenetic | 180 |
| abstract_inverted_index.sufficiently | 81 |
| abstract_inverted_index.effectiveness | 53 |
| abstract_inverted_index.environmental | 4, 123 |
| abstract_inverted_index.metabarcoding | 5, 36, 198 |
| abstract_inverted_index.Nanopore-based | 35 |
| abstract_inverted_index.revolutionised | 7 |
| cited_by_percentile_year | |
| countries_distinct_count | 2 |
| institutions_distinct_count | 5 |
| citation_normalized_percentile.value | 0.44642171 |
| citation_normalized_percentile.is_in_top_1_percent | False |
| citation_normalized_percentile.is_in_top_10_percent | False |