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On the limits of computational functional genomics for bacterial lifestyle prediction
2014
Briefings in Functional Genomics
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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
2012
Computer applications in the biosciences : CABIOS
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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
2021
GigaScience
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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
2018
BMC Evolutionary Biology
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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
2012
PLoS ONE
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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
2018
Viruses
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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
2020
PLoS Computational Biology
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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
2021
BMC Microbiology
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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
2006
Journal of Molecular Microbiology and Biotechnology
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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
2011
PLoS ONE
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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
2020
The ISME Journal
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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
2009
Biology Direct
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., 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
2015
BMC Genomics
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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
2010
Journal of Bacteriology
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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
2020
PLoS Computational Biology
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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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