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Article: Mining traits for the enrichment and isolation of not-yet-cultured populations

TitleMining traits for the enrichment and isolation of not-yet-cultured populations
Authors
Zhang, ANMao, YWang, YZhang, T
KeywordsEnrichment and isolation
Bioinformatic pipeline
Pan-genome analysis
Metabolisms
Not-yet-cultured bacteria
Issue Date2019
PublisherBioMed Central Ltd. The Journal's web site is located at http://www.microbiomejournal.com/
Citation
Microbiome, 2019, v. 7 n. 1, p. article no. 96 How to Cite?
DOI: http://dx.doi.org/10.1186/s40168-019-0708-4
AbstractBackground: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. Results: Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. Conclusion: Our method could shed light to the exploration into the bacterial dark matter in the environments.
Persistent Identifierhttp://hdl.handle.net/10722/293579
ISSN
2049-2618
2023 Impact Factor: 13.8
2023 SCImago Journal Rankings: 3.802
PubMed Central ID
PMC6593511
ISI Accession Number ID
WOS:000472969500001

 

DC FieldValueLanguage
dc.contributor.authorZhang, AN-
dc.contributor.authorMao, Y-
dc.contributor.authorWang, Y-
dc.contributor.authorZhang, T-
dc.date.accessioned2020-11-23T08:18:49Z-
dc.date.available2020-11-23T08:18:49Z-
dc.date.issued2019-
dc.identifier.citationMicrobiome, 2019, v. 7 n. 1, p. article no. 96-
dc.identifier.issn2049-2618-
dc.identifier.urihttp://hdl.handle.net/10722/293579-
dc.description.abstractBackground: The lack of pure cultures limits our understanding into 99% of bacteria. Proper interpretation of the genetic and the transcriptional datasets can reveal clues for the enrichment and even isolation of the not-yet-cultured populations. Unraveling such information requires a proper mining method. Results: Here, we present a method to infer the hidden traits for the enrichment of not-yet-cultured populations. We demonstrate this method using Candidatus Accumulibacter. Our method constructs a whole picture of the carbon, electron, and energy flows in the not-yet-cultured populations from the genomic datasets. Then, it decodes the coordination across three flows from the transcriptional datasets. Based on it, our method diagnoses the status of the not-yet-cultured populations and provides strategy to optimize the enrichment systems. Conclusion: Our method could shed light to the exploration into the bacterial dark matter in the environments.-
dc.languageeng-
dc.publisherBioMed Central Ltd. The Journal's web site is located at http://www.microbiomejournal.com/-
dc.relation.ispartofMicrobiome-
dc.rightsMicrobiome. Copyright © BioMed Central Ltd.-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.subjectEnrichment and isolation-
dc.subjectBioinformatic pipeline-
dc.subjectPan-genome analysis-
dc.subjectMetabolisms-
dc.subjectNot-yet-cultured bacteria-
dc.titleMining traits for the enrichment and isolation of not-yet-cultured populations-
dc.typeArticle-
dc.identifier.emailZhang, T: zhangt@hkucc.hku.hk-
dc.identifier.authorityZhang, T=rp00211-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1186/s40168-019-0708-4-
dc.identifier.pmid31238973-
dc.identifier.pmcidPMC6593511-
dc.identifier.scopuseid_2-s2.0-85068141539-
dc.identifier.hkuros319437-
dc.identifier.volume7-
dc.identifier.issue1-
dc.identifier.spagearticle no. 96-
dc.identifier.epagearticle no. 96-
dc.identifier.isiWOS:000472969500001-
dc.publisher.placeUnited Kingdom-
dc.identifier.issnl2049-2618-

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