scholarly journals Metabolic marker gene mining provides insight in globalmcrAdiversity and, coupled with targeted genome reconstruction, sheds further light on metabolic potential of theMethanomassiliicoccales

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5614 ◽  
Author(s):  
Daan R. Speth ◽  
Victoria J. Orphan

Over the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through themcrAgene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of theMethanomassiliicoccalesand reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an uncultivated environmental clade of theMethanomassiliicoccales. Analysis of the ‘Lake Pavin cluster’ draft genome suggests that this organism has a more restricted capacity for hydrogenotrophic methylotrophic methanogenesis than previously studiedMethanomassiliicoccales, with only genes for growth on methanol present. However, the presence of the soluble subunits of methyltetrahydromethanopterin:CoM methyltransferase (mtrAH)provide hypothetical pathways for methanol fermentation, and aceticlastic methanogenesis that await experimental verification. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.

2018 ◽  
Author(s):  
Daan R. Speth ◽  
Victoria J. Orphan

AbstractOver the past years, metagenomics has revolutionized our view of microbial diversity. Moreover, extracting near-complete genomes from metagenomes has led to the discovery of known metabolic traits in unsuspected lineages. Genome-resolved metagenomics relies on assembly of the sequencing reads and subsequent binning of assembled contigs, which might be hampered by strain heterogeneity or low abundance of a target organism. Here we present a complementary approach, metagenome marker gene mining, and use it to assess the global diversity of archaeal methane metabolism through the mcrA gene. To this end, we have screened 18,465 metagenomes for the presence of reads matching a database representative of all known mcrA proteins and reconstructed gene sequences from the matching reads. We use our mcrA dataset to assess the environmental distribution of theMethanomassiliicoccalesand reconstruct and analyze a draft genome belonging to the ‘Lake Pavin cluster’, an understudied environmental clade of theMethanomassiliicoccales. Thus, we show that marker gene mining can enhance the discovery power of metagenomics, by identifying novel lineages and aiding selection of targets for in-depth analyses. Marker gene mining is less sensitive to strain heterogeneity and has a lower abundance threshold than genome-resolved metagenomics, as it only requires short contigs and there is no binning step. Additionally, it is computationally cheaper than genome resolved metagenomics, since only a small subset of reads needs to be assembled. It is therefore a suitable approach to extract knowledge from the many publicly available sequencing projects.


Author(s):  
Bennett J Kapili ◽  
Anne E Dekas

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.


2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Bo Liu ◽  
Guo-Hong Liu ◽  
Yu-jing Zhu ◽  
Jie-Ping Wang ◽  
Jian-Mei Che ◽  
...  

Here, we report the draft genome sequences of Bacillus drentensis DSM 15600 T and Bacillus novalis DSM 15603 T with 5,305,306 bp and 5,667,584 bp, respectively, which will provide useful information for the functional gene mining and application of these two species. The average DNA G+C contents were 38.91% and 40.01%, respectively.


Author(s):  
Simon Horobin

‘Authorities’ considers how the rules of usage are established. It first describes the role of dictionaries, frequently held to be the ultimate authority. It then discusses linguistic academies, governing bodies that make pronouncements about correct usage. An alternative source to the dictionary is the usage guide, which tends to adopt a more prescriptive approach and which focuses on a small subset of frequently disputed points of usage. Other ways of determining acceptability is to turn to examples of actual usage, logic, or etymology. Despite the many controversies concerning correct usage and how it should be established, each of the authorities discussed would agree that there is a single authoritative form of the language, known as Standard English.


2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Guo-hong Liu ◽  
Bo Liu ◽  
Yu-jing Zhu ◽  
Jie-ping Wang ◽  
Jian-mei Che ◽  
...  

Bacillus mesonae FJAT-13985 T is a Gram-positive, spore-forming, and aerobic bacterium. Here, we report the draft genome sequence of B. mesonae FJAT-13985 T with 5,807,726 bp, which will provide useful information for setting up phylogenomics in the genomic taxonomy of the Bacillus -like bacteria, as well as for the functional gene mining and application of B. mesonae FJAT-13985 T .


2019 ◽  
Vol 8 (29) ◽  
Author(s):  
Denis S. Grouzdev ◽  
Salimat K. Bidzhieva ◽  
Diyana S. Sokolova ◽  
Tatiyana P. Tourova ◽  
Andrey B. Poltaraus ◽  
...  

The draft genome sequence of a mesophilic fermenting bacterium, Soehngenia sp. strain 1933P, isolated from production water of the Binagady petroleum reservoir (Republic of Azerbaijan), is presented. The genome is annotated for elucidation of the metabolic potential and taxonomic position of strain 1933P.


2020 ◽  
Vol 21 (24) ◽  
pp. 9363
Author(s):  
Gillian Li Yin Lee ◽  
Nur Nadhirah Zakaria ◽  
Peter Convey ◽  
Hiroyuki Futamata ◽  
Azham Zulkharnain ◽  
...  

Study of the potential of Antarctic microorganisms for use in bioremediation is of increasing interest due to their adaptations to harsh environmental conditions and their metabolic potential in removing a wide variety of organic pollutants at low temperature. In this study, the psychrotolerant bacterium Rhodococcus sp. strain AQ5-07, originally isolated from soil from King George Island (South Shetland Islands, maritime Antarctic), was found to be capable of utilizing phenol as sole carbon and energy source. The bacterium achieved 92.91% degradation of 0.5 g/L phenol under conditions predicted by response surface methodology (RSM) within 84 h at 14.8 °C, pH 7.05, and 0.41 g/L ammonium sulphate. The assembled draft genome sequence (6.75 Mbp) of strain AQ5-07 was obtained through whole genome sequencing (WGS) using the Illumina Hiseq platform. The genome analysis identified a complete gene cluster containing catA, catB, catC, catR, pheR, pheA2, and pheA1. The genome harbours the complete enzyme systems required for phenol and catechol degradation while suggesting phenol degradation occurs via the β-ketoadipate pathway. Enzymatic assay using cell-free crude extract revealed catechol 1,2-dioxygenase activity while no catechol 2,3-dioxygenase activity was detected, supporting this suggestion. The genomic sequence data provide information on gene candidates responsible for phenol and catechol degradation by indigenous Antarctic bacteria and contribute to knowledge of microbial aromatic metabolism and genetic biodiversity in Antarctica.


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