Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

Czech, Lucas; Barbera, Pierre; Stamatakis, Alexandros

doi:10.1093/bioinformatics/btaa070

Cited by 238 publications

(141 citation statements)

References 26 publications

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“…Read placement into a reference tree is a promising approach that increases accuracy and precision in metabarcoding studies compared to OTU clustering and BLAST-based amplicon variant read mapping (Stark et al 2010;Berger et al 2011;Matsen et al 2012;Paul et al 2018;Czech et al 2018Czech et al , 2019Barbera et al 2019;Carbone et al 2019). The method, also dubbed phylogenetic binning, relies on three components: (1) a reference tree for a set of taxa which can be derived through phylogenetic analysis of existing data; (2) a fixed alignment of reference sequences corresponding to the metabarcoding marker (e.g.…”

Section: Multiple Alignment-based Read Placementmentioning

confidence: 99%

“…Read placement also allows the implementation of quantitative species delimitation methods to automatically assess taxonomic diversity, an approach already integrated into the phylogenetic binning approach (Zhang et al 2013). Broad reference trees can be assembled and centrally maintained to be used in analytical pipelines (Tedersoo et al 2018a;Carbone et al 2019), or alternatively computed automatically from published sequences (Czech et al 2019), allowing dynamic on-the-fly solutions for particular situations.…”

Section: Multiple Alignment-based Read Placementmentioning

confidence: 99%

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Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

et al. 2020

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True fungi (Fungi) and fungus-like organisms (e.g. Mycetozoa, Oomycota) constitute the second largest group of organisms based on global richness estimates, with around 3 million predicted species. Compared to plants and animals, fungi have simple body plans with often morphologically and ecologically obscure structures. This poses challenges for accurate and precise identifications. Here we provide a conceptual framework for the identification of fungi, encouraging the approach of integrative (polyphasic) taxonomy for species delimitation, i.e. the combination of genealogy (phylogeny), phenotype (including autecology), and reproductive biology (when feasible). This allows objective evaluation of diagnostic characters, either phenotypic or molecular or both. Verification of identifications is crucial but often neglected. Because of clade-specific evolutionary histories, there is currently no single tool for the identification of fungi, although DNA barcoding using the internal transcribed spacer (ITS) remains a first diagnosis, particularly in metabarcoding studies. Secondary DNA barcodes are increasingly implemented for groups where ITS does not provide sufficient precision. Issues of pairwise sequence similarity-based identifications and OTU clustering are discussed, and multiple sequence alignment-based phylogenetic approaches with subsequent verification are recommended as more accurate alternatives. In metabarcoding approaches, the trade-off between speed and accuracy and precision of molecular identifications must be carefully considered. Intragenomic variation of the ITS and other barcoding markers should be properly documented, as phylotype diversity is not necessarily a proxy of species richness. Important strategies to improve molecular identification of fungi are: (1) broadly document intraspecific and intragenomic variation of barcoding markers; (2) substantially expand sequence repositories, focusing on undersampled clades and missing taxa; (3) improve curation of sequence labels in primary repositories and substantially increase the number of sequences based on verified material; (4) link sequence data to digital information of voucher specimens including imagery. In parallel, technological improvements to genome sequencing offer promising alternatives to DNA barcoding in the future. Despite the prevalence of DNA-based fungal taxonomy, phenotype-based approaches remain an important strategy to catalog the global diversity of fungi and establish initial species hypotheses.

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Section: Multiple Alignment-based Read Placementmentioning

confidence: 99%

Section: Multiple Alignment-based Read Placementmentioning

confidence: 99%

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

et al. 2020

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“…One way the gut microbiome can influence host physiology is through the generation of soluble metabolites that can cross the intestinal mucosa and enter circulation 22 . PICRUSt2 was used to impute the metagenomic contents of the gut microbiota from 16S-seq abundances [23][24][25][26][27] (Fig. 5A).…”

Section: Co-occurrence and Mutual Exclusion Network Analysis Revealsmentioning

confidence: 99%

Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the gastrointestinal tract

Johanson

Goertz

Marin

et al. 2020

Sci Rep

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The gut microbiome is known to be sensitive to changes in the immune system, especially during autoimmune diseases such as Multiple Sclerosis (MS). Our study examines the changes to the gut microbiome that occur during experimental autoimmune encephalomyelitis (EAE), an animal model for MS. We collected fecal samples at key stages of EAE progression and quantified microbial abundances with 16S V3–V4 amplicon sequencing. Our analysis of the data suggests that the abundance of commensal Lactobacillaceae decreases during EAE while other commensal populations belonging to the Clostridiaceae, Ruminococcaceae, and Peptostreptococcaceae families expand. Community analysis with microbial co-occurrence networks points to these three expanding taxa as potential mediators of gut microbiome dysbiosis. We also employed PICRUSt2 to impute MetaCyc Enzyme Consortium (EC) pathway abundances from the original microbial abundance data. From this analysis, we found that a number of imputed EC pathways responsible for the production of immunomodulatory compounds appear to be enriched in mice undergoing EAE. Our analysis and interpretation of results provides a detailed picture of the changes to the gut microbiome that are occurring throughout the course of EAE disease progression and helps to evaluate EAE as a viable model for gut dysbiosis in MS patients.

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“…To improve the predictions, we used NSTI scores lower than 1. Phylogenetic placement of reads was done using the EPA-NG ( 68 ) and Gappa ( 69 ) tools. The Castor R package ( 70 ) was used to predict the gene family abundances.…”

Section: Methodsmentioning

confidence: 99%

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

Díaz-García

Huang

Spröer

et al. 2021

Appl Environ Microbiol

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The engineering of complex communities can be a successful path to understand the ecology of microbial systems and improve biotechnological processes. Here, we developed a strategy to assemble a minimal and effective lignocellulolytic microbial consortium (MELMC) using a sequential combination of dilution-to-stimulation and dilution-to-extinction approaches. The consortium was retrieved from Andean forest soil and selected through incubation in liquid media with a mixture of three types of agricultural plant residues. After the dilution-to-stimulation phase, approximately 50 bacterial sequence types, mostly belonging to the Sphingobacteriaceae, Enterobacteriaceae, Pseudomonadaceae and Paenibacillaceae, were significantly enriched. The dilution-to-extinction method demonstrated that only eight of the bacterial sequence types were necessary to maintain microbial growth and plant biomass consumption. After a subsequent stabilization, only two bacterial species (Pseudomonas sp. and Paenibacillus sp.) became highly abundant (> 99%) within the MELMC, indicating that these are the key players of degradation. Differences in the composition of bacterial communities between biological replicates indicated that selection, sampling and/or priority effects could shape the consortium structure. The MELMC can degrade up to ∼13% of corn stover, consuming mostly its (hemi)cellulosic fraction. Tests with chromogenic substrates showed that the MELMC secrete an array of endo-enzymes able to degrade xylan, arabinoxylan, carboxymethyl cellulose and wheat straw. Additionally, the metagenomic profile inferred from the phylogenetic composition next to an analysis of carbohydrate-active enzymes of twenty bacterial genomes supports the potential of the MELMC to deconstruct plant polysaccharides. This capacity was mainly attributed to the presence of Paenibacillus sp. IMPORTANCE The significance of our study mainly lies on the development of a combined top-down enrichment strategy (i.e. dilution-to-stimulation coupled to dilution-to-extinction) to build a minimal and versatile lignocellulolytic microbial consortium. We demonstrated that mainly two selectively enriched bacterial species (Pseudomonas sp. and Paenibacillus sp.) are required to drive an effective degradation of plant polymers. Our findings can guide the design of a synthetic bacterial consortium that could improve saccharification (i.e. release of sugars from agricultural plant residues) processes in biorefineries. In addition, they can help to expand our ecological understanding of plant biomass degradation in enriched bacterial systems.

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Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

Cited by 238 publications

References 26 publications

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?

Experimental autoimmune encephalomyelitis is associated with changes of the microbiota composition in the gastrointestinal tract

Dilution-to-Stimulation/Extinction Method: a Combination Enrichment Strategy To Develop a Minimal and Versatile Lignocellulolytic Bacterial Consortium

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