Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

Forster, Dominik; Lentendu, Guillaume; Filker, Sabine; Dubois, Elyssa; Wilding, Thomas A.; Stoeck, Thorsten

doi:10.1111/1462-2920.14764

Cited by 43 publications

(53 citation statements)

References 86 publications

(159 reference statements)

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“…We used both the original ASV data and ASV-clusters for downstream analysis. This ASV-clustering approach was preferred over the traditional OTU clustering: ASVs reduce false positive rates more than most OTU clustering approaches and therefore result in a more accurate phylogenetic tree and more accurate, tractable clusters [57][58][59][60] .…”

Section: Methodsmentioning

confidence: 99%

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

Grembi

Nguyen

Haggerty

et al. 2020

Sci Rep

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While low-carbohydrate and low-fat diets can both lead to weight-loss, a substantial variability in achieved long-term outcomes exists among obese but otherwise healthy adults. We examined the hypothesis that structural differences in the gut microbiota explain a portion of variability in weight-loss using two cohorts of obese adults enrolled in the Diet Intervention Examining The Factors Interacting with Treatment Success (DIETFITS) study. A total of 161 pre-diet fecal samples were sequenced from a discovery cohort (n = 66) and 106 from a validation cohort (n = 56). An additional 157 fecal samples were sequenced from the discovery cohort after 10 weeks of dietary intervention. We found no specific bacterial signatures associated with weight loss that were consistent across both cohorts. However, the gut microbiota plasticity (i.e. variability), was correlated with long-term (12-month) weight loss in a diet-dependent manner; on the low-fat diet subjects with higher pre-diet daily plasticity had higher sustained weight loss, whereas on the low-carbohydrate diet those with higher plasticity over 10 weeks of dieting had higher 12-month weight loss. Our findings suggest the potential importance of gut microbiota plasticity for sustained weight-loss. We highlight the advantages of evaluating kinetic trends and assessing reproducibility in studies of the gut microbiota.

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Section: Methodsmentioning

confidence: 99%

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

Grembi

Nguyen

Haggerty

et al. 2020

Sci Rep

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“…Forster et al . () processed haplotypes of 29 ciliate species with DADA2 (Callahan et al ., ) and SWARM (Mahé et al ., ) and observed that both methods required additional haplotype grouping to reach congruency with morphological data. Results of Dunthorn et al .…”

Section: Discussionmentioning

confidence: 99%

Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity

Gaonkar

Piredda

Sarno

et al. 2020

Environmental Microbiology

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High-throughput sequencing (HTS) metabarcoding is commonly applied to assess phytoplankton diversity. Usually, haplotypes are grouped into operational taxonomic units (OTUs) through clustering, whereby the resulting number of OTUs depends on chosen similarity thresholds. We applied, instead, a phylogenetic approach to infer taxa among 18S rDNA V4-metabarcode haplotypes gathered from 48 time-series samples using the marine planktonic diatoms Chaetoceros and Bacteriastrum as test case. The 73 recovered taxa comprised both solitary haplotypes and polytomies, the latter composed each of a highly abundant, dominant haplotype and one to several minor, peripheral haplotypes. The solitary and dominant haplotypes usually matched reference sequences, enabling species assignation of taxa. We hypothesise that the super-abundance of reads in dominant haplotypes results from the homogenization effect of concerted evolution. Reads of populous peripheral haplotypes and dominant haplotypes show comparable distribution patterns over the sample dates, suggesting that they are part of the same population. Many taxa revealed marked seasonality, with closely related ones generally showing distinct periodicity, whereas others occur year-round. Phylogenies inferred from metabarcode haplotypes enable delineation of biologically meaningful taxa, whereas OTUs resulting from clustering algorithms often deviate markedly from such taxa.

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“…Many of the novel or rare OTUs mentioned above could be artifacts produced during sequencing and/or sequence grouping, and thus, additional postclustering quality filters are recommended (Forster et al. ; Frøslev et al. ).…”

Section: What Have We Learned With and About Metabarcoding?mentioning

confidence: 99%

Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

Santoferrara

Burki

Filker

et al. 2020

J Eukaryotic Microbiology

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During the last decade, high‐throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on short DNA sequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up‐to‐date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding.

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Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

Cited by 43 publications

References 86 publications

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention

Species detection and delineation in the marine planktonic diatoms Chaetoceros and Bacteriastrum through metabarcoding: making biological sense of haplotype diversity

Perspectives from Ten Years of Protist Studies by High‐Throughput Metabarcoding

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