SIP-Metaproteomics: Linking Microbial Taxonomy, Function, and Activity

2019 ◽  
pp. 57-69
Author(s):  
Martin Taubert
Keyword(s):  
Microbial Taxonomy

PPIT: an R package for inferring microbial taxonomy from nifH sequences

2021 ◽  
Author(s):  
Bennett J Kapili ◽  
Anne E Dekas
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Query Sequence ◽  
Marker Gene ◽  
R Package ◽  
Supplementary Information ◽  
Marker Genes ◽  
Pairwise Identity ◽  
Metabolic Marker ◽  
Microbial Taxonomy

Abstract Motivation Linking microbial community members to their ecological functions is a central goal of environmental microbiology. When assigned taxonomy, amplicon sequences of metabolic marker genes can suggest such links, thereby offering an overview of the phylogenetic structure underpinning particular ecosystem functions. However, inferring microbial taxonomy from metabolic marker gene sequences remains a challenge, particularly for the frequently sequenced nitrogen fixation marker gene, nitrogenase reductase (nifH). Horizontal gene transfer in recent nifH evolutionary history can confound taxonomic inferences drawn from the pairwise identity methods used in existing software. Other methods for inferring taxonomy are not standardized and require manual inspection that is difficult to scale. Results We present Phylogenetic Placement for Inferring Taxonomy (PPIT), an R package that infers microbial taxonomy from nifH amplicons using both phylogenetic and sequence identity approaches. After users place query sequences on a reference nifH gene tree provided by PPIT (n = 6317 full-length nifH sequences), PPIT searches the phylogenetic neighborhood of each query sequence and attempts to infer microbial taxonomy. An inference is drawn only if references in the phylogenetic neighborhood are: (1) taxonomically consistent and (2) share sufficient pairwise identity with the query, thereby avoiding erroneous inferences due to known horizontal gene transfer events. We find that PPIT returns a higher proportion of correct taxonomic inferences than BLAST-based approaches at the cost of fewer total inferences. We demonstrate PPIT on deep-sea sediment and find that Deltaproteobacteria are the most abundant potential diazotrophs. Using this dataset we show that emending PPIT inferences based on visual inspection of query sequence placement can achieve taxonomic inferences for nearly all sequences in a query set. We additionally discuss how users can apply PPIT to the analysis of other marker genes. Availability PPIT is freely available to non-commercial users at https://github.com/bkapili/ppit. Installation includes a vignette that demonstrates package use and reproduces the nifH amplicon analysis discussed here. The raw nifH amplicon sequence data have been deposited in the GenBank, EMBL, and DDBJ databases under BioProject number PRJEB37167. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Microbial Taxonomy Run Amok

2021 ◽  
Vol 29 (5) ◽  
pp. 394-404 ◽  
Author(s):  
Robert A. Sanford ◽  
Karen G. Lloyd ◽  
Konstantinos T. Konstantinidis ◽  
Frank E. Löffler
Keyword(s):  
Microbial Taxonomy

Microbial taxonomy in the era of OMICS: application of DNA sequences, computational tools and techniques

2017 ◽  
Vol 110 (10) ◽  
pp. 1357-1371 ◽  
Author(s):  
Nitish Kumar Mahato ◽  
Vipin Gupta ◽  
Priya Singh ◽  
Rashmi Kumari ◽  
Helianthous Verma ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Computational Tools ◽  
Microbial Taxonomy ◽  
Tools And Techniques

scholarly journals A Bayesian compositional estimator for microbial taxonomy based on biomarkers

2008 ◽  
Vol 6 (5) ◽  
pp. 190-199 ◽  
Author(s):  
Karel Van den Meersche ◽  
Karline Soetaert ◽  
Jack J. Middelburg
Keyword(s):  
Microbial Taxonomy

scholarly journals Editorial: Microbial Taxonomy, Phylogeny and Biodiversity

2019 ◽  
Vol 10 ◽  
Author(s):  
Jesús L. Romalde ◽  
Sabela Balboa ◽  
Antonio Ventosa
Keyword(s):  
Microbial Taxonomy

scholarly journals Reads2Type: a web application for rapid microbial taxonomy identification

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Dhany Saputra ◽  
Simon Rasmussen ◽  
Mette V. Larsen ◽  
Nizar Haddad ◽  
Maria Maddalena Sperotto ◽  
...  
Keyword(s):  
Web Application ◽  
Microbial Taxonomy

When should a DDH experiment be mandatory in microbial taxonomy?

2013 ◽  
Vol 195 (6) ◽  
pp. 413-418 ◽  
Author(s):  
Jan P. Meier-Kolthoff ◽  
Markus Göker ◽  
Cathrin Spröer ◽  
Hans-Peter Klenk
Keyword(s):  
Microbial Taxonomy

scholarly journals A Dictionary of Microbial Taxonomy

1979 ◽  
Vol 32 (3) ◽  
pp. 309-309
Author(s):  
G. I. Barrow
Keyword(s):  
Microbial Taxonomy

On the fitness of microbial taxonomy

2012 ◽  
Vol 20 (11) ◽  
pp. 514-516 ◽  
Author(s):  
Javier Tamames ◽  
Ramon Rosselló-Móra
Keyword(s):  
Microbial Taxonomy

Regulation of Citrate Synthase and Microbial Taxonomy

Nature ◽  
1968 ◽  
Vol 219 (5151) ◽  
pp. 270-272 ◽  
Author(s):  
P. D. J. WEITZMAN ◽  
DOROTHY JONES
Keyword(s):  
Citrate Synthase ◽  
Microbial Taxonomy
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