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On the limits of computational functional genomics for bacterial lifestyle prediction

E. Barbosa, R. Rottger, A.-C. Hauschild, V. Azevedo, J. Baumbach
2014 Briefings in Functional Genomics  
As they occupy various niches in diverse habitats, one may assume the existence of lifestyle-specific genomic features.  ...  We review the level of genomic specificity regarding actinobacterial pathogenicity.  ...  The aim of this paper was to investigate the power of computational functional genomics to predict bacterial lifestyles utilizing DNA sequence information only.  ... 
doi:10.1093/bfgp/elu014 pmid:24855068 fatcat:tlydn7uayzctljsdnq3jxqdfoi

PHACTS, a computational approach to classifying the lifestyle of phages

Katelyn McNair, Barbara A. Bailey, Robert A. Edwards
2012 Computer applications in the biosciences : CABIOS  
Therefore, a computational method that utilizes the sequence data of phage genomes is needed.  ...  Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology.  ...  Funding: Advances in Bioinformatics from the National Science Foundation (grant DBI 0850356). Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/bts014 pmid:22238260 pmcid:PMC3289917 fatcat:m3t74qilyrcozkteyvrc43r2iq

DeePhage: distinguishing virulent and temperate phage-derived sequences in metavirome data with a deep learning approach

Shufang Wu, Zhencheng Fang, Jie Tan, Mo Li, Chunhui Wang, Qian Guo, Congmin Xu, Xiaoqing Jiang, Huaiqiu Zhu
2021 GigaScience  
On real metavirome, DeePhage correctly predicts the highest proportion of contigs when using BLAST as annotation, without apparent preferences.  ...  The accuracy of DeePhage on 5-fold cross-validation reaches as high as 89%, nearly 10% and 30% higher than that of 2 similar tools, PhagePred and PHACTS.  ...  Part of the analysis was performed on the High Performance Computing Platform of the Center for Life Science of Peking University.  ... 
doi:10.1093/gigascience/giab056 pmid:34498685 pmcid:PMC8427542 fatcat:g3rawspd25huvgnq4zbeicmsay

Factors driving effective population size and pan-genome evolution in bacteria

Louis-Marie Bobay, Howard Ochman
2018 BMC Evolutionary Biology  
Results: In this study, we estimated Ne for 153 species (152 bacteria and one archaeon) defined under a common framework and found that ecological lifestyle and growth rate were major predictors of Ne;  ...  Knowledge of population-level processes is essential to understanding the efficacy of selection operating within a species.  ...  Acknowledgments We thank Alexei Wirganowicz for assistance in the analyses of gene turnover and Kim Hammond for assistance in the preparation of figures.  ... 
doi:10.1186/s12862-018-1272-4 pmid:30314447 pmcid:PMC6186134 fatcat:kmtlq36nkbdyjmnfb2ujyh43by

Metabolic Networks of Sodalis glossinidius: A Systems Biology Approach to Reductive Evolution

Eugeni Belda, Francisco J. Silva, Juli Peretó, Andrés Moya, Christos A. Ouzounis
2012 PLoS ONE  
Meanwhile, reductive evolution simulations on the extant metabolic network can predict possible future evolution of S. glossinidius in the context of genome reduction.  ...  Results: The functional profile of ancestral and extant metabolic networks sheds light on the evolutionary events underlying transition to a host-dependent lifestyle.  ...  In the absence of this kind of information for S. glossinidius, we adopted the biomass equation defined for E. coli K12 as objective function for FBA simulations on the metabolic networks [38] .  ... 
doi:10.1371/journal.pone.0030652 pmid:22292008 pmcid:PMC3265509 fatcat:3wnhoibl2vcnbaq4xznbnmcghe

Characterizing Phage Genomes for Therapeutic Applications

Casandra Philipson, Logan Voegtly, Matthew Lueder, Kyle Long, Gregory Rice, Kenneth Frey, Biswajit Biswas, Regina Cer, Theron Hamilton, Kimberly Bishop-Lilly
2018 Viruses  
One limiting factor is a lack of guidelines for assessing the genomic safety of phage candidates.  ...  The feasibility and utility of the pipeline is demonstrated on two new phage genomes that meet all safety criteria.  ...  To circumvent the limitations of functional annotation we combine our analysis with PHACTS, a classification algorithm that predicts phage lifestyle based on the entire phage proteome.  ... 
doi:10.3390/v10040188 pmid:29642590 pmcid:PMC5923482 fatcat:36uvchktg5byvjbe6kojq3kv5m

Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling

Cristina Herencias, Sergio Salgado-Briegas, María A. Prieto, Juan Nogales, Vassily Hatzimanikatis
2020 PLoS Computational Biology  
Overall, we present here a valuable computational testbed based on predatory bacteria activity for rational design of novel and controlled biocatalysts in biotechnological/clinical applications.  ...  We provide computational evidences supporting potential axenic growth of B. bacteriovorus's in a rich medium based on its encoded metabolic capabilities.  ...  Acknowledgments The authors thank Clive A. Dove for critical reading of the manuscript. PLOS COMPUTATIONAL BIOLOGY Genome-scale metabolic modeling of B. bacteriovorus  ... 
doi:10.1371/journal.pcbi.1007646 pmid:32925899 fatcat:eit6dnlj3zb2dnwv7yuvxyidgi

Application of machine learning in bacteriophage research

Yousef Nami, Nazila Imeni, Bahman Panahi
2021 BMC Microbiology  
On the other hand, with the advent of new high-throughput sequencing technology, the development of a powerful computational framework to characterize the newly identified bacteriophages is inevitable  ...  Moreover, potential limitations and advantages of the developed frameworks were discussed.  ...  Although, limited experimented data is a major drawback for traditional in silico approaches, Machine learning approaches provided a promising avenue to predict the functions of phage proteins [26, 50  ... 
doi:10.1186/s12866-021-02256-5 pmid:34174831 pmcid:PMC8235560 fatcat:dfgscfyh5bfoxg7nhlpvpgpy6q

The Bioinformatic Study of Transmembrane Molecular Transport

Milton H. Saier Jr., Qinghu Ren
2006 Journal of Molecular Microbiology and Biotechnology  
Out of the hundreds of thousands of proteins encoded in bacterial, archaeal and eukaryotic genomes, over 10% function in transport.  ...  Currently over 300 fully sequenced genomes are available for analysis. Many of the encoded transporters have been classified into different families, and their functions have been predicted.  ... 
doi:10.1159/000095630 pmid:17114892 fatcat:5d7glt37sjatlmdosxamv267ee

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

John M. Chaston, Garret Suen, Sarah L. Tucker, Aaron W. Andersen, Archna Bhasin, Edna Bode, Helge B. Bode, Alexander O. Brachmann, Charles E. Cowles, Kimberly N. Cowles, Creg Darby, Limaris de Léon (+45 others)
2011 PLoS ONE  
Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence  ...  Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological  ...  Acknowledgments We would like to thank Joanne McAndrews for editing the manuscript. This paper is dedicated to the late Nancy Leimgruber.  ... 
doi:10.1371/journal.pone.0027909 pmid:22125637 pmcid:PMC3220699 fatcat:vstusooztzbadntwdurann3f6u

Insights into the dynamics between viruses and their hosts in a hot spring microbial mat

Jessica K. Jarett, Mária Džunková, Frederik Schulz, Simon Roux, David Paez-Espino, Emiley Eloe-Fadrosh, Sean P. Jungbluth, Natalia Ivanova, John R. Spear, Stephanie A. Carr, Christopher B. Trivedi, Frank A. Corsetti (+5 others)
2020 The ISME Journal  
Our current knowledge of host-virus interactions in biofilms is limited to computational predictions based on laboratory experiments with a small number of cultured bacteria.  ...  Thirty-four out of 130 single cells contained at least one viral contig (26%), which, together with the metagenome-assembled genomes, resulted in detection of 59 viruses linked to 34 host species.  ...  We also thank Janey Lee for preparing the illustrations for Fig. 1 , and Heather Maughan for proofreading and comments on the final version of the manuscript.  ... 
doi:10.1038/s41396-020-0705-4 pmid:32661357 pmcid:PMC7490370 fatcat:yb4n2foybfbxnbljfewpxkx2zi

Massive comparative genomic analysis reveals convergent evolution of specialized bacteria

Vicky Merhej, Manuela Royer-Carenzi, Pierre Pontarotti, Didier Raoult
2009 Biology Direct  
., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle  ...  The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles.  ...  Pardoux for advice on statistical analyses, C. Notredame and P-E. Fournier for discussions and comments on the manuscript, and S. Audic and G. Fournous for technical support.  ... 
doi:10.1186/1745-6150-4-13 pmid:19361336 pmcid:PMC2688493 fatcat:ifijc724gzhrrnp2wqme4i5z5m

Using the taxon-specific genes for the taxonomic classification of bacterial genomes

Ankit Gupta, Vineet K Sharma
2015 BMC Genomics  
This approach has been implemented for the development of a tool 'Microtaxi' which can be used for the taxonomic assignment of complete bacterial genomes.  ...  The complete genome sequencing of a bacterial genome often reveals a substantial number of unique genes present only in that genome which can be used for its taxonomic classification.  ...  Acknowledgements We thank MHRD, Govt of India, funded Centre for Research on Environment and Sustainable Technologies (CREST) at IISER Bhopal for its support.  ... 
doi:10.1186/s12864-015-1542-0 pmid:25990029 pmcid:PMC4438512 fatcat:w4bd24a3x5dbvam54owbprtyuq

Complete Genome Sequence of the Metabolically Versatile Plant Growth-Promoting Endophyte Variovorax paradoxus S110

J.-I. Han, H.-K. Choi, S.-W. Lee, P. M. Orwin, J. Kim, S. L. LaRoe, T.-g. Kim, J. O'Neil, J. R. Leadbetter, S. Y. Lee, C.-G. Hur, J. C. Spain (+3 others)
2010 Journal of Bacteriology  
The complete genome sequence of V. paradoxus S110 is composed of 6,754,997 bp with 6,279 predicted protein-coding sequences within two circular chromosomes.  ...  Genomic analysis has revealed multiple metabolic features for autotrophic and heterotrophic lifestyles. These metabolic diversities enable independent survival, as well as a symbiotic lifestyle.  ...  ACKNOWLEDGMENTS We thank all of the people involved in this project. We especially thank an anonymous reviewer for helpful comments.  ... 
doi:10.1128/jb.00925-10 pmid:21183664 pmcid:PMC3067606 fatcat:qrpzm2aunvclhjdnbbsjgsfwr4

A systematic pipeline for classifying bacterial operons reveals the evolutionary landscape of biofilm machineries

Cedoljub Bundalovic-Torma, Gregory B. Whitfield, Lindsey S. Marmont, P. Lynne Howell, John Parkinson, Mark M. Tanaka
2020 PLoS Computational Biology  
Despite the fundamental importance that these mechanisms play in bacterial environmental adaptation, a systematic approach for studying the evolution of operon organization is lacking.  ...  Herein, we present a novel method to study the evolution of operons based on phylogenetic clustering of operon-encoded protein families and genomic-proximity network visualizations of operon architectures  ...  The number of bacterial genomes with different combinations of predicted EPS operons, further represented with their distribution (% bacterial genomes) across different lifestyles and environmental niches  ... 
doi:10.1371/journal.pcbi.1007721 pmid:32236097 fatcat:m6d773w2w5horjqupsdpf7rciu
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