Benchmarking de métodos de binning a partir de un metagenoma conceptual

106 p.La metagenómica implica el estudio de comunidades microbianas enteras mediante el muestreo directo y la secuenciación de los genomas presentes en un entorno determinado. En los últimos años, la disponibilidad de secuencias metagenomicas ha crecido de manera significativa, debido principalmente al enorme impacto de las tecnologías de secuenciación de nueva generación (NGS). A diferencia del análisis clásico de un genoma, que implica la manipulación y ensamble de un número moderado de lecturas (20,000 – 30,000) largas (650-800 pb), la metagenómica tiene el reto de analizar millones de lecturas cortas (35-250 pb) de múltiples microorganismos, muchos de los cuales se desconocen. Uno de los problemas subyacentes del análisis metagenómico es la recuperación de los genomas individuales presentes en la muestra en estudio. La clasificación y el agrupamiento de lecturas o contigs de NGS en unidades taxonómicas operacionales putativos se conoce como binning. Varios métodos de bioinformática para binning se han descrito en los últimos años. Estos métodos se basan en principios diferentes (dependientes de la taxonomía e independientes de la taxonomía) y los softwares se ejecutan de forma local o a través de un servicio web. A pesar de la diversidad de métodos, no hay consenso sobre cuál es el mejor. Con esto en mente, 11 de los métodos de agrupación disponibles han sido evaluados utilizando un metagenoma conceptual construido con el software Grinder (*). Este metagenoma incluye 9 genomas procariontes completamente secuenciados y 28 genomas virales de diversa filiación taxonómica, consta de 2,5 millones de lecturas. El rendimiento de los softwares de binning se evaluó a través de cuatro criterios (el porcentaje de bases clasificadas, el porcentaje de bases correctamente clasificadas, el puntaje taxonómico y la distancia de la variación de la información). Los métodos de clasificación se evaluaron para todo el conjunto de datos, y las fracciones microbianas y virales. * //sourceforge.net/projects/biogrinder/ Se evaluaron cuarenta y siete programas de binning diferentes. De estos: 18 resultaron ser obsoletos, 16 fueron limitados en su aplicación y 13 estaban funcionales para realizar binning. De este último grupo, 2 no fueron evaluados por razones técnicas, dejando a 11 programas de binning que fueron evaluados en profundidad. Estos programas fueron clasificados de acuerdo a los criterios antes mencionados. Los tres programas de binning mejor evaluados fueron: DiScRIBinATE, MEGAN y Sort-ITEMS. El ranking completo se muestra en la Tabla 24./ABSTRACT: Metagenomics entails the study of entire microbial communities via direct sampling and sequencing of genomes present in a given environment. In recent years, the availability of metagenomic sequences has grown significantly, mainly due to the enormous impact of Next Generation Sequencing (NGS) technologies. Unlike classical genome analysis involving the handling and assembly of a moderate number (20,000 – 30,000) of long reads (650-800 bp), metagenomics is challenged to analyze millions of short reads (35-250 bp) of multiple microorganisms, many of which are unknown.One of the underlying problems of metagenomic analysis is the retrieval of the individual genomes present in the sample under study. Classification and grouping of NGS reads or contigs into putative operational taxonomic units is known as binning. Several bioinformatics methods for binning have been described in recent years. These methods are based on different principles (taxonomy dependent and taxonomy independent) and executable programs are run either locally or through a web service. Despite the diversity of methods there is no consensus on which is best.With this in mind, 11 of the available binning methods have been benchmarked using a conceptual metagenome built with Grinder (*). This metagenome includes 9 completely sequenced prokaryotic and 28 viral genomes of diverse taxonomic affiliation and consists of 2.5 million reads. The binning performance of each softwares was evaluated and ranked through four criteria (percent of classified bases, percent of correctly classified bases, taxonomic score and distance of variation of information). Best scoring methods for the whole data set, and the microbial and viral fractions are sourceforge.net/projects/biogrinder/ Fourty-seven different softwares programs for binning were evaluated. Of these: 18 were found to be obsolete, 16 were limited in their application and 13 were determined to be suitable for metagenomic binning. Of this latter group, 2 were not evaluated further for technical reasons, leaving 11 softwares programs that were evaluated in depth. These programs were ranked according to the aforementioned criteria. The top three programs according to correct binning were: DiScRIBinATE, MEGAN and SOrt-ITEMS. The complete ranking is shown in “Tabla 24”

Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile

Indexación: Web of Science; PubMedLeptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod- shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0142-

Molecular systematics of the genus Acidithiobacillus:insights into the phylogenetic structure and diversification of the taxon

The acidithiobacilli are sulfur-oxidizing acidophilic bacteria that thrive in both natural and anthropogenic low pH environments. They contribute to processes that lead to the generation of acid rock drainage in several different geoclimatic contexts, and their properties have long been harnessed for the biotechnological processing of minerals. Presently, the genus is composed of seven validated species, described between 1922 and 2015: Acidithiobacillus thiooxidans, A. ferrooxidans, A. albertensis, A. caldus, A. ferrivorans, A. ferridurans, and A. ferriphilus. However, a large number of Acidithiobacillus strains and sequence clones have been obtained from a variety of ecological niches over the years, and many isolates are thought to vary in phenotypic properties and cognate genetic traits. Moreover, many isolates remain unclassified and several conflicting specific assignments muddle the picture from an evolutionary standpoint. Here we revise the phylogenetic relationships within this species complex and determine the phylogenetic species boundaries using three different typing approaches with varying degrees of resolution: 16S rRNA gene-based ribotyping, oligotyping, and multi-locus sequencing analysis (MLSA). To this end, the 580 16S rRNA gene sequences affiliated to the Acidithiobacillus spp. were collected from public and private databases and subjected to a comprehensive phylogenetic analysis. Oligotyping was used to profile high-entropy nucleotide positions and resolve meaningful differences between closely related strains at the 16S rRNA gene level. Due to its greater discriminatory power, MLSA was used as a proxy for genome-wide divergence in a smaller but representative set of strains. Results obtained indicate that there is still considerable unexplored diversity within this genus. At least six new lineages or phylotypes, supported by the different methods used herein, are evident within the Acidithiobacillus species complex. Although the diagnostic characteristics of these subgroups of strains are as yet unresolved, correlations to specific metadata hint to the mechanisms behind econiche-driven divergence of some of the species/phylotypes identified. The emerging phylogenetic structure for the genus outlined in this study can be used to guide isolate selection for future population genomics and evolutionary studies in this important acidophile model

Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus ‘ Igneacidithiobacillus’

Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is ‘Igneacidithiobacillus’, a novel genus-level taxon, represented by ‘Igneacidithiobacillus copahuensis’ VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including ‘Ca. Igneacidithiobacillus chanchocoensis’ (mCHCt20-1TS), ‘Igneacidithiobacillus siniensis’ (S30A2T), ‘Ca. Igneacidithiobacillus taupoensis’ (TVZ-G3 TS), and ‘Ca. Igneacidithiobacillus waiarikiensis’ (TVZ-G4 TS). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus ‘Igneacidithiobacillus’

Draft genome sequence of the type strain of the sulfur-oxidizing acidophile, Acidithiobacillus albertensis (DSM 14366)

Abstract Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus. The assembled genome is 3,1 Mb, and contains 47 tRNAs, tmRNA gene and 2 rRNA operons, along with 3149 protein-coding predicted genes. The Whole Genome Shotgun project was deposited in DDBJ/EMBL/GenBank under the accession MOAD00000000

The phylogeny of Acetobacteraceae: photosynthetic traits and deranged respiratory enzymes

Comprehensive phylogenomic analysis of the Acetobacteracea

Metagenome-derived draft genome sequence of acidithiobacillus ferrooxidans RV1 from an abandoned gold tailing in neuquén, Argentina

In this work we report the metagenome-derived draft genomic sequence of an enrichment culture dominated by A. ferrooxidans obtained from an airlift bioreactor inoculated with the microbial consortium recovered from the “Relave Viejo” tailing. The genome of this culture was assembled de-novo and by reference, generating a consensus assembly of 3.0 Mb. On the basis of 16S rRNA (100 % identity), average nucleotide identity analysis (99.33% identity) and in silico DNA-DNA hybridization against A. ferrooxidans ATCC 23270T (97.9%), the recovered genome is confirmed to pertain to A. ferrooxidans species. Comparative genomics results are presented to uncover the genetic traits of the variant surviving lime treatment and to further explore the genomic diversity of these model iron oxidizing species.Fil: Ulloa, José Ricardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas. Universidad Nacional del Comahue. Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas; ArgentinaFil: Moya Beltrán, Ana. Fundación Ciencia & Vida; ChileFil: Issotta, Francisco. Fundación Ciencia & Vida; ChileFil: Nuñez, Harold. Fundación Ciencia & Vida; ChileFil: Covarrubias, Paulo C.. Fundación Ciencia & Vida; ChileFil: Donati, Edgardo Ruben. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Centro de Investigación y Desarrollo en Fermentaciones Industriales. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Centro de Investigación y Desarrollo en Fermentaciones Industriales; ArgentinaFil: Quatrini, Raquel. Fundación Ciencia & Vida; ChileFil: Giaveno Filippa, Maria Alejandra. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Patagonia Norte. Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas. Universidad Nacional del Comahue. Instituto de Investigación y Desarrollo en Ingeniería de Procesos, Biotecnología y Energías Alternativas; Argentin

Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile

Abstract Acidithiobacillus thiooxidans CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. A. thiooxidans plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution. CLST is a strain of A. thiooxidans able to tolerate moderate chloride concentrations (up to 15 g L−1 Cl−), a feature that is quite unusual in extreme acidophilic microorganisms. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 3,974,949 bp draft genome is arranged into 40 scaffolds of 389 contigs containing 3866 protein-coding genes and 75 RNAs encoding genes. This is the first draft genome of a halotolerant A. thiooxidans strain. The release of the genome sequence of this strain improves representation of these extreme acidophilic Gram negative bacteria in public databases and strengthens the framework for further investigation of the physiological diversity and ecological function of A. thiooxidans populations

Additional file 1: Figure S1. of Draft genome sequence of Acidithiobacillus thiooxidans CLST isolated from the acidic hypersaline Gorbea salt flat in northern Chile

(A, C) A. thiooxidans ATCC 19377 cell growth and growth specific rate with and without NaCl. (B, D) A. thiooxidans CLST cell growth and growth specific rate with and without NaCl. (TIFF 272 kb