Microbial systematics and taxonomy: relevance for a microbial commons

Moore, Edward R. B.; Mihaylova, Sashka; Vandamme, Peter; Krichevsky, Micah I.; Dijkshoorn, Lenie

doi:10.1016/j.resmic.2010.05.007

Cited by 69 publications

(65 citation statements)

References 33 publications

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“…On the other hand, the Genome BLAST Distance Phylogeny (GBDP) strategy considers the whole genome sequence and a global comparison is made using alignment tools such as BLAT or BLAST (Basic Local Alignment Search Tool) (Chun and Rainey 2014). Another genomic approach for taxonomic assignment is the characterization of DNA fragments and their variations, which can be restriction sites, insertions and deletions, DNA sequence repeats or microsatellites, single nucleotide polymorphisms or other sequence variations (Moore et al 2010). Amplified fragment length polymorphism (AFLP) has also proven useful for the delineation of new species (Nemec et al 2001).…”

Section: Asignación De Taxonesmentioning

confidence: 99%

“…Amplified fragment length polymorphism (AFLP) has also proven useful for the delineation of new species (Nemec et al 2001). In order to apply as much information as possible to obtain the most accurate characterization possible, taxonomic assignment protocols using other molecules and a polyphasic approach, including MALD-TOF mass spectrometry (Ramasamy et al 2014), have also been proposed (Moore et al 2010). The most commonly used techniques and the level of taxonomic resolution are shown in figure 2.…”

Section: Asignación De Taxonesmentioning

confidence: 99%

“…Por otro lado, la determinación de la distancia filogénica por comparación de genomas (GBDP: Genome BLAST Distance Phylogeny) es una estrategia que considera la secuencia genómica completa y se realiza una comparación global mediante un alineamiento local con herramientas como BLAST o BLAT (Chun y Rainey 2014). Otra estrategia genómica para la asignación taxonómica es la caracterización de fragmentos de ADN y sus variaciones, que pueden ser sitios de restricción, inserciones, supresiones, secuencias repetidas o microsatélites, polimorfismos de una sola base u otras diferencias de las secuencias (Moore et al 2010). La detección de polimorfismo del tamaño de fragmentos amplificados (AFLP: amplified fragment length polymorphism) ha mostrado ser útil para la delineación de nuevas especies (Nemec et al 2001).…”

Section: Specific Databasesunclassified

“…La detección de polimorfismo del tamaño de fragmentos amplificados (AFLP: amplified fragment length polymorphism) ha mostrado ser útil para la delineación de nuevas especies (Nemec et al 2001). Con la intención de utilizar la mayor información posible e incrementar la precisión en la caracterización, también se han propuesto protocolos de asignación de taxones con otras moléculas y con un enfoque polifásico (Moore et al 2010) mediante espectrometría de masas (Ramasamy et al 2014). Las técnicas más utilizadas para la asignación taxonómica y el nivel de resolución que permiten se presentan en la figura 2.…”

Section: Specific Databasesunclassified

“…Si bien ambas bases de datos Figure 2. Methodology for the characterization of prokaryotes and the different levels of taxonomic resolution (modified from Moore et al 2010). Figura 2.…”

Section: Bases De Datos Generalesmentioning

confidence: 99%

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The 16S rRNA gene in the study of marine microbial communities

et al. 2015

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ABSTRACT. New sequencing technologies and analytical capabilities have stimulated the study of microbial communities from specific environments, enabling researchers to understand the complexity of those systems. The 16S rRNA gene has proved very useful in describing the diversity and characterization of marine microbial communities, particularly of uncultivated organisms. The development of new sequencing techniques has contributed to the exponential increase in the number of reported 16S rRNA sequences as barcodes for microorganisms, forcing a review of concepts and methods for the taxonomic classification of these organisms. Manipulation and analysis of large amounts of genetic information have prompted the development of specific databases, specialized algorithms, and computational tools to compare thousands of such sequences and make a taxonomic assignment. Complete 16S rRNA sequences are thus needed for accurate and reproducible taxonomy assignment in the study of marine bacterial communities.Key words: metagenomics, marine microbial communities, 16S rRNA databases. RESUMEN. Las nuevas tecnologías de secuenciación y capacidades analíticas han estimulado el estudio de las comunidades microbianas deambientes específicos, lo cual ha permitido conocer la complejidad de estos sistemas. El gen ARNr 16S ha demostrado ser de gran utilidad para describir y caracterizar las comunidades microbianas marinas, especialmente los organismos no cultivados. Las nuevas técnicas de secuenciación han contribuido al incremento exponencial de registro de secuencias, aunque parciales, del ARNr 16S como elemento de código de barras para microorganismos. Consecuentemente, ha sido necesaria una revisión de conceptos y métodos de clasificación taxonómica para estos organismos. El manejo y análisis de una gran cantidad de información génica han impulsado el desarrollo de bases de datos específicas, algoritmos y herramientas computacionales especializadas para comparar miles de secuencias semejantes y hacer la asignación taxonómica. Por lo tanto, las secuencias completas del ARNr 16S son necesarias para una asignación taxonómica certera y reproducible en los estudios de comunidades microbianas marinas.Palabras clave: metagenómica, comunidades microbianas marinas, bases de datos ARNr 16S.

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Section: Asignación De Taxonesmentioning

confidence: 99%

Section: Asignación De Taxonesmentioning

confidence: 99%

Section: Specific Databasesunclassified

“…Si bien ambas bases de datos Figure 2. Methodology for the characterization of prokaryotes and the different levels of taxonomic resolution (modified from Moore et al 2010). Figura 2.…”

Section: Bases De Datos Generalesmentioning

confidence: 99%

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The 16S rRNA gene in the study of marine microbial communities

et al. 2015

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Proteotyping

Karlsson

Gonzales-Silès

Boulund

et al. 2017

MALDI‐TOF and Tandem MS for Clinical Microbiology

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Robinsoniella

Lawson¹

2018

Bergey's Manual of Systematics of Archaea and Bacteria

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Ro.bin.so.ni.el'la. N.L. fem. dim. n. Robinsoniella in honor of Isadore M. Robinson, in recognition of his many contributions to swine microbiology. Firmicutes / Clostridia / Clostridiales / Lachnospiraceae / Robinsoniella Gram‐stain‐positive, ovoid to short rods occurring as single cells or in pairs. Endospores are formed. Anaerobic. Growth is observed with glucose in addition to a range of carbohydrates. The major end products of metabolism include acetate and succinate, but no butyrate is detected. The cell‐wall murein is based on meso ‐diaminopimelic acid as the diagnostic diamino acid. No respiratory quinones are detected. Polar lipids include an aminophosphoglycolipid, an aminophospholipid, diphosphatidylglycerol, glycolipids, phospholipids, phosphatidylethanolamine, and phosphatidylglycerol. The major long‐chain cellular fatty acid profile consists of a complex mixture of straight‐chain saturated, monounsaturated, and iso ‐methyl‐branched acids. Member of the class Clostridia , family Lachnospiraceae . Known habitats are feces of human and animals and human clinical sources. DNA G + C content (mol%) : Approximately 48.7 (HPLC); approximately 41 (WGS). Type species : Robinsoniella peoriensis Cotta, Whitehead, Falsen, Moore and Lawson 2009, 154 VP .

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Microbial systematics and taxonomy: relevance for a microbial commons

Cited by 69 publications

References 33 publications

The 16S rRNA gene in the study of marine microbial communities

The 16S rRNA gene in the study of marine microbial communities

Proteotyping

Robinsoniella

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