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Functional gene-guided enrichment plus in situ microsphere cultivation enables isolating new crucial ureolytic bacteria from the rumen of cattle

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Title: Functional gene-guided enrichment plus in situ microsphere cultivation enables isolating new crucial ureolytic bacteria from the rumen of cattle
Authors: Liu, Sijia, Yu, Zhongtang, Zhong, Huiyue, Zheng, Nan, Huws, Sharon, Wang, Jiaqi, Zhao, Shengguo
Source: Liu, S, Yu, Z, Zhong, H, Zheng, N, Huws, S, Wang, J & Zhao, S 2023, 'Functional gene-guided enrichment plus in situ microsphere cultivation enables isolating new crucial ureolytic bacteria from the rumen of cattle', Microbiome, vol. 11, 76. https://doi.org/10.1186/s40168-023-01510-4
Publication Year: 2023
Collection: Queen's University Belfast: Research Portal
Subject Terms: Rumen, Urease - genetics - metabolism, Amino Acids - metabolism, Isolation, Bacteria, Urease, Animals, Urea - metabolism, Rumen - microbiology, Nitrogen - metabolism, Ureolytic bacteria, Agarose microsphere embedding, Ruminants - metabolism, In situ cultivation, Cattle, Microspheres
Description: Background Ruminants can utilize urea as a dietary nitrogen source owing to their ability to recycle urea-N back to the rumen where numerous ureolytic bacteria hydrolyze urea into ammonia, which is used by numerous bacteria as their nitrogen source. Rumen ureolytic bacteria are the key microbes making ruminants the only type of animals independent of pre-formed amino acids for survival, thus having attracted much research interest. Sequencing-based studies have helped gain new insights into ruminal ureolytic bacterial diversity, but only a limited number of ureolytic bacteria have been isolated into pure cultures or studied, hindering the understanding of ureolytic bacteria with respect to their metabolism, physiology, and ecology, all of which are required to effectively improve urea-N utilization efficiency. Results We established and used an integrated approach, which include urease gene (ureC) guided enrichment plus in situ agarose microsphere embedding and cultivation under rumen-simulating conditions, to isolate ureolytic bacteria from the rumen microbiome. We optimized the dilutions of the rumen microbiome during the enrichment, single-cell embedding, and then in situ cultivation of microsphere-embedded bacteria using dialysis bags placed in rumen fluid. Metabonomic analysis revealed that the dialysis bags had a fermentation profile very similar to the simulated rumen fermentation. In total, we isolated 404 unique strains of bacteria, of which 52 strains were selected for genomic sequencing. Genomic analyses revealed that 28 strains, which were classified into 12 species, contained urease genes. All these ureolytic bacteria represent new species ever identified in the rumen and represented the most abundant ureolytic species. Compared to all the previously isolated ruminal ureolytic species combined, the newly isolated ureolytic bacteria increased the number of genotypically and phenotypically characterized ureolytic species by 34.38% and 45.83%, respectively. These isolated strains have unique genes ...
Document Type: article in journal/newspaper
File Description: application/pdf
Language: English
ISSN: 2049-2618
Relation: info:eu-repo/semantics/altIdentifier/pmid/37060083; info:eu-repo/semantics/altIdentifier/pissn/2049-2618
DOI: 10.1186/s40168-023-01510-4
Availability: https://pure.qub.ac.uk/en/publications/1cfa3a80-3682-4026-9f5c-68919d6146be
https://doi.org/10.1186/s40168-023-01510-4
https://pureadmin.qub.ac.uk/ws/files/460188149/s40168_023_01510_4.pdf
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  Data: Functional gene-guided enrichment plus in situ microsphere cultivation enables isolating new crucial ureolytic bacteria from the rumen of cattle
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  Data: <searchLink fieldCode="AR" term="%22Liu%2C+Sijia%22">Liu, Sijia</searchLink><br /><searchLink fieldCode="AR" term="%22Yu%2C+Zhongtang%22">Yu, Zhongtang</searchLink><br /><searchLink fieldCode="AR" term="%22Zhong%2C+Huiyue%22">Zhong, Huiyue</searchLink><br /><searchLink fieldCode="AR" term="%22Zheng%2C+Nan%22">Zheng, Nan</searchLink><br /><searchLink fieldCode="AR" term="%22Huws%2C+Sharon%22">Huws, Sharon</searchLink><br /><searchLink fieldCode="AR" term="%22Wang%2C+Jiaqi%22">Wang, Jiaqi</searchLink><br /><searchLink fieldCode="AR" term="%22Zhao%2C+Shengguo%22">Zhao, Shengguo</searchLink>
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  Data: Liu, S, Yu, Z, Zhong, H, Zheng, N, Huws, S, Wang, J & Zhao, S 2023, 'Functional gene-guided enrichment plus in situ microsphere cultivation enables isolating new crucial ureolytic bacteria from the rumen of cattle', Microbiome, vol. 11, 76. https://doi.org/10.1186/s40168-023-01510-4
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  Data: <searchLink fieldCode="DE" term="%22Rumen%22">Rumen</searchLink><br /><searchLink fieldCode="DE" term="%22Urease+-+genetics+-+metabolism%22">Urease - genetics - metabolism</searchLink><br /><searchLink fieldCode="DE" term="%22Amino+Acids+-+metabolism%22">Amino Acids - metabolism</searchLink><br /><searchLink fieldCode="DE" term="%22Isolation%22">Isolation</searchLink><br /><searchLink fieldCode="DE" term="%22Bacteria%22">Bacteria</searchLink><br /><searchLink fieldCode="DE" term="%22Urease%22">Urease</searchLink><br /><searchLink fieldCode="DE" term="%22Animals%22">Animals</searchLink><br /><searchLink fieldCode="DE" term="%22Urea+-+metabolism%22">Urea - metabolism</searchLink><br /><searchLink fieldCode="DE" term="%22Rumen+-+microbiology%22">Rumen - microbiology</searchLink><br /><searchLink fieldCode="DE" term="%22Nitrogen+-+metabolism%22">Nitrogen - metabolism</searchLink><br /><searchLink fieldCode="DE" term="%22Ureolytic+bacteria%22">Ureolytic bacteria</searchLink><br /><searchLink fieldCode="DE" term="%22Agarose+microsphere+embedding%22">Agarose microsphere embedding</searchLink><br /><searchLink fieldCode="DE" term="%22Ruminants+-+metabolism%22">Ruminants - metabolism</searchLink><br /><searchLink fieldCode="DE" term="%22In+situ+cultivation%22">In situ cultivation</searchLink><br /><searchLink fieldCode="DE" term="%22Cattle%22">Cattle</searchLink><br /><searchLink fieldCode="DE" term="%22Microspheres%22">Microspheres</searchLink>
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  Data: Background Ruminants can utilize urea as a dietary nitrogen source owing to their ability to recycle urea-N back to the rumen where numerous ureolytic bacteria hydrolyze urea into ammonia, which is used by numerous bacteria as their nitrogen source. Rumen ureolytic bacteria are the key microbes making ruminants the only type of animals independent of pre-formed amino acids for survival, thus having attracted much research interest. Sequencing-based studies have helped gain new insights into ruminal ureolytic bacterial diversity, but only a limited number of ureolytic bacteria have been isolated into pure cultures or studied, hindering the understanding of ureolytic bacteria with respect to their metabolism, physiology, and ecology, all of which are required to effectively improve urea-N utilization efficiency. Results We established and used an integrated approach, which include urease gene (ureC) guided enrichment plus in situ agarose microsphere embedding and cultivation under rumen-simulating conditions, to isolate ureolytic bacteria from the rumen microbiome. We optimized the dilutions of the rumen microbiome during the enrichment, single-cell embedding, and then in situ cultivation of microsphere-embedded bacteria using dialysis bags placed in rumen fluid. Metabonomic analysis revealed that the dialysis bags had a fermentation profile very similar to the simulated rumen fermentation. In total, we isolated 404 unique strains of bacteria, of which 52 strains were selected for genomic sequencing. Genomic analyses revealed that 28 strains, which were classified into 12 species, contained urease genes. All these ureolytic bacteria represent new species ever identified in the rumen and represented the most abundant ureolytic species. Compared to all the previously isolated ruminal ureolytic species combined, the newly isolated ureolytic bacteria increased the number of genotypically and phenotypically characterized ureolytic species by 34.38% and 45.83%, respectively. These isolated strains have unique genes ...
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        Value: 10.1186/s40168-023-01510-4
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      – Text: English
    Subjects:
      – SubjectFull: Rumen
        Type: general
      – SubjectFull: Urease - genetics - metabolism
        Type: general
      – SubjectFull: Amino Acids - metabolism
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      – SubjectFull: Nitrogen - metabolism
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      – SubjectFull: Ureolytic bacteria
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      – SubjectFull: Agarose microsphere embedding
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      – SubjectFull: In situ cultivation
        Type: general
      – SubjectFull: Cattle
        Type: general
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      – TitleFull: Functional gene-guided enrichment plus in situ microsphere cultivation enables isolating new crucial ureolytic bacteria from the rumen of cattle
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