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Hill-based dissimil...
Hill-based dissimilarity indices and null models for analysis of microbial community assembly
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- Modin, Oskar, 1980 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Liebana, Raquel, 1986 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Saheb Alam, Soroush, 1986 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Wilen, Britt-Marie, 1966 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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- Suarez, Carolina (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,University of Gothenburg
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- Hermansson, Malte, 1954 (författare)
- Gothenburg University,Göteborgs universitet,Institutionen för kemi och molekylärbiologi,Department of Chemistry and Molecular Biology,University of Gothenburg
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- Persson, Frank, 1970 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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(creator_code:org_t)
- 2020-09-11
- 2020
- Engelska.
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Ingår i: Microbiome. - : Springer Science and Business Media LLC. - 2049-2618. ; 8:1
- Relaterad länk:
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https://research.cha... (primary) (free)
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https://gup.ub.gu.se...
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https://doi.org/10.1...
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Abstract
Ämnesord
Stäng
- BackgroundHigh-throughput amplicon sequencing of marker genes, such as the 16S rRNA gene in Bacteria and Archaea, provides a wealth of information about the composition of microbial communities. To quantify differences between samples and draw conclusions about factors affecting community assembly, dissimilarity indices are typically used. However, results are subject to several biases, and data interpretation can be challenging. The Jaccard and Bray-Curtis indices, which are often used to quantify taxonomic dissimilarity, are not necessarily the most logical choices. Instead, we argue that Hill-based indices, which make it possible to systematically investigate the impact of relative abundance on dissimilarity, should be used for robust analysis of data. In combination with a null model, mechanisms of microbial community assembly can be analyzed. Here, we also introduce a new software, qdiv, which enables rapid calculations of Hill-based dissimilarity indices in combination with null models.ResultsUsing amplicon sequencing data from two experimental systems, aerobic granular sludge (AGS) reactors and microbial fuel cells (MFC), we show that the choice of dissimilarity index can have considerable impact on results and conclusions. High dissimilarity between replicates because of random sampling effects make incidence-based indices less suited for identifying differences between groups of samples. Determining a consensus table based on count tables generated with different bioinformatic pipelines reduced the number of low-abundant, potentially spurious amplicon sequence variants (ASVs) in the data sets, which led to lower dissimilarity between replicates. Analysis with a combination of Hill-based indices and a null model allowed us to show that different ecological mechanisms acted on different fractions of the microbial communities in the experimental systems.ConclusionsHill-based indices provide a rational framework for analysis of dissimilarity between microbial community samples. In combination with a null model, the effects of deterministic and stochastic community assembly factors on taxa of different relative abundances can be systematically investigated. Calculations of Hill-based dissimilarity indices in combination with a null model can be done in qdiv, which is freely available as a Python package (https://github.com/omvatten/qdiv). In qdiv, a consensus table can also be determined from several count tables generated with different bioinformatic pipelines.
Ämnesord
- NATURVETENSKAP -- Biologi -- Mikrobiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Microbiology (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Samhällsbyggnadsteknik -- Vattenteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Civil Engineering -- Water Engineering (hsv//eng)
- NATURVETENSKAP -- Biologi -- Ekologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Ecology (hsv//eng)
- NATURVETENSKAP -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
- NATURAL SCIENCES -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Miljöbioteknik -- Vattenbehandling (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Environmental Biotechnology -- Water Treatment (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Miljöbioteknik -- Annan miljöbioteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Environmental Biotechnology -- Other Environmental Biotechnology (hsv//eng)
Nyckelord
- Aerobic granular sludge
- Amplicon sequencing
- Beta diversity
- Bioinformatics
- Microbial ecology
- Microbial fuel cell
- measuring beta-diversity
- differentiation measures
- phylogenetic
- diversity
- similarity
- sequences
- entropy
- Microbiology
- Microbial ecology
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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Modin, Oskar, 19 ...
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Liebana, Raquel, ...
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Saheb Alam, Soro ...
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Wilen, Britt-Mar ...
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Suarez, Carolina
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Hermansson, Malt ...
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visa fler...
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Persson, Frank, ...
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visa färre...
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- NATURVETENSKAP
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Microbiome
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Göteborgs universitet
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Chalmers tekniska högskola