Functional Changes of the Community of Microbes With Ni-Dependent Enzyme Genes Accompany Adaptation of the Ruminal Microbiome to Urea-Supplemented Diets
Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have...
Saved in:
Published in | Frontiers in microbiology Vol. 11; p. 596681 |
---|---|
Main Authors | , , , , |
Format | Journal Article |
Language | English |
Published |
Switzerland
Frontiers Media S.A
22.12.2020
|
Subjects | |
Online Access | Get full text |
Cover
Loading…
Abstract | Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have therefore investigated changes in the ruminal microbiome and its community with Ni-dependent enzyme genes following urea supplementation and analyzed the associations of rumen environmental factors, including fermentation variables and Ni concentrations, with the compositional and functional changes of these communities. We found that urea supplementation increased urease activity and the concentrations of ammonia and Ni, and tended to increase concentrations of short chain fatty acids and acetate, whereas it decreased rumen pH and the L-/D-lactate ratio. With standards for genome completeness >60% and strain heterogeneity <10%, 20 bacterial species containing five Ni-dependent enzyme genes were detected in the metagenome sequences. For the five Ni-dependent enzyme genes, urea supplementation increased the relative abundances of genes of urease and acetyl-CoA synthase, whereas it decreased the relative abundances of genes of glyoxalase I, [NiFe]-hydrogenase, and lactate racemase. For the 20 microbes with Ni-dependent enzyme genes, urea supplementation increased the relative abundances of five bacteria exhibiting high capacities for the utilization of hemicellulose and pectin for butyrate and fatty acid biosynthesis. For the ruminal microbiome, urea supplementation increased the metagenomic capacities for hemicellulose and pectin degradation, butyrate generation, fatty acid biosynthesis, and carbon fixation, whereas it decreased the metagenomic capacities for starch degradation, propionate generation, and sulfur and nitrogen metabolism. Constrained correspondence analysis identified rumen ammonia and Ni concentrations as likely driving factors in the reshaping of the ruminal microbiome and, together with pH, of the community of microbes with Ni-dependent enzyme genes. Thus, the functional change of the latter community is probably an important event in the adaptation of the ruminal microbiome to urea-supplemented diets. This result provides a new perspective for the understanding of the effects of urea supplementation on rumen fermentation. |
---|---|
AbstractList | Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which require Ni as a catalyst for ureolysis. The key event in the changes of the ruminal microbiome after urea supplementation remains unknown. We have therefore investigated changes in the ruminal microbiome and its community with Ni-dependent enzyme genes following urea supplementation and analyzed the associations of rumen environmental factors, including fermentation variables and Ni concentrations, with the compositional and functional changes of these communities. We found that urea supplementation increased urease activity and the concentrations of ammonia and Ni, and tended to increase concentrations of short chain fatty acids and acetate, whereas it decreased rumen pH and the L-/D-lactate ratio. With standards for genome completeness >60% and strain heterogeneity <10%, 20 bacterial species containing five Ni-dependent enzyme genes were detected in the metagenome sequences. For the five Ni-dependent enzyme genes, urea supplementation increased the relative abundances of genes of urease and acetyl-CoA synthase, whereas it decreased the relative abundances of genes of glyoxalase I, [NiFe]-hydrogenase, and lactate racemase. For the 20 microbes with Ni-dependent enzyme genes, urea supplementation increased the relative abundances of five bacteria exhibiting high capacities for the utilization of hemicellulose and pectin for butyrate and fatty acid biosynthesis. For the ruminal microbiome, urea supplementation increased the metagenomic capacities for hemicellulose and pectin degradation, butyrate generation, fatty acid biosynthesis, and carbon fixation, whereas it decreased the metagenomic capacities for starch degradation, propionate generation, and sulfur and nitrogen metabolism. Constrained correspondence analysis identified rumen ammonia and Ni concentrations as likely driving factors in the reshaping of the ruminal microbiome and, together with pH, of the community of microbes with Ni-dependent enzyme genes. Thus, the functional change of the latter community is probably an important event in the adaptation of the ruminal microbiome to urea-supplemented diets. This result provides a new perspective for the understanding of the effects of urea supplementation on rumen fermentation. |
Author | Shen, Hong Lu, Zhongyan Kong, Lingmeng Aschenbach, Jörg R Xu, Zhihui |
AuthorAffiliation | 1 Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China 4 Institute of Veterinary Physiology, Freie Universität Berlin , Berlin , Germany 2 College of Life Sciences, Nanjing Agricultural University , Nanjing , China 3 Bioinformatics Center, Nanjing Agricultural University , Nanjing , China |
AuthorAffiliation_xml | – name: 4 Institute of Veterinary Physiology, Freie Universität Berlin , Berlin , Germany – name: 1 Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China – name: 2 College of Life Sciences, Nanjing Agricultural University , Nanjing , China – name: 3 Bioinformatics Center, Nanjing Agricultural University , Nanjing , China |
Author_xml | – sequence: 1 givenname: Zhongyan surname: Lu fullname: Lu, Zhongyan organization: Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China – sequence: 2 givenname: Zhihui surname: Xu fullname: Xu, Zhihui organization: Bioinformatics Center, Nanjing Agricultural University, Nanjing, China – sequence: 3 givenname: Lingmeng surname: Kong fullname: Kong, Lingmeng organization: College of Life Sciences, Nanjing Agricultural University, Nanjing, China – sequence: 4 givenname: Hong surname: Shen fullname: Shen, Hong organization: Bioinformatics Center, Nanjing Agricultural University, Nanjing, China – sequence: 5 givenname: Jörg R surname: Aschenbach fullname: Aschenbach, Jörg R organization: Institute of Veterinary Physiology, Freie Universität Berlin, Berlin, Germany |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/33414773$$D View this record in MEDLINE/PubMed |
BookMark | eNpVkstu1DAUhi1UREvpA7BBWbLJYMdO4myQRtMLlQpIQAU768Q5nnGV2CFxkIYn6ePWadqq9cbWuXy_j_2_JQfOOyTkPaMrzmX1yXRW16uMZnSVV0Uh2StyxIpCpJxmfw6enQ_JyTje0LhELKb0DTnkXDBRlvyI3J5PTgfrHbTJZgdui2PiTRJ2mGx8103Ohv0c-Gr14OuY_G3DLvlm01Ps0TXoQnLm_u87TC7QxfRaa9_14PbJuoE-wIx-BP6YOjvrLCzrY1PwyfWAkP6c-r7FLuKwSU4thvEdeW2gHfHkYT8m1-dnvzZf0qvvF5eb9VWqRZGH1MTR8xoMA6wErzXDEkuuoTa6pKyqjMwllXVVc9GwUiBURYaSMyZz5FhJfkwuF27j4Ub1g-1g2CsPVt0H_LBVMASrW1QF40XRNBSopALRSAkiE3kdJZiBikXW54XVT3WHjY7jDNC-gL7MOLtTW_9PlaXMRFZFwMcHwOD_TjgG1dlRY9uCQz-NKhNlkce_FiKWsqU0vuU4DmieZBhVs0HUvUHUbBC1GCT2fHh-v6eORzvwO3LNvBo |
CitedBy_id | crossref_primary_10_1016_j_bej_2022_108656 crossref_primary_10_1016_j_jhazmat_2023_132504 crossref_primary_10_1093_femsre_fuab057 crossref_primary_10_3389_fmicb_2022_851567 |
Cites_doi | 10.1080/17450399609381898 10.2527/2000.781188x 10.1128/iai.73.11.7252-7258.2005 10.1371/journal.pone.0017288 10.1007/s00253-017-8323-4 10.3168/jds.s0022-0302(77)83990-8 10.1111/j.1365-2672.1986.tb03761.x 10.1038/nmeth.3103 10.2527/jas.2014-8214 10.1074/jbc.m111.251603 10.1128/aem.33.5.1097-1104.1977 10.1007/s00248-012-0007-0 10.1093/nar/gkh340 10.2527/jas1971.324769x 10.1007/bf00394042 10.2527/jas1988.6692313x 10.2527/jas.2008-0912 10.1111/1462-2920.12457 10.1371/journal.pone.0117811 10.1038/nmeth.1923 10.1016/j.abb.2013.09.002 10.1093/ansci/82.3.884 10.2527/jas1980.503527x 10.1016/j.jinorgbio.2007.07.014 10.3389/fmicb.2019.02038 10.1007/s12011-018-1524-6 10.2527/jas1978.4761345x 10.1101/gr.186072.114 10.1128/aem.64.10.3854-3859.1998 10.1080/17450397709440608 10.1186/1471-2180-1-5 10.3389/fmicb.2017.00385 10.1038/srep19175 10.3168/jds.s0022-0302(91)78551-2 10.1093/bioinformatics/bts174 10.1093/sysbio/syq010 10.1128/iai.70.2.685-691.2002 10.2527/jas.2011-3854 10.1016/s0168-6445(03)00042-1 10.1093/nar/gkq747 10.1093/nar/gkm321 10.1017/s0003356100004992 10.2527/jas.2010-3301 10.1021/cr4004488 10.1371/journal.pone.0061217 10.2527/jas1987.643887x 10.1002/jsfa.8177 10.1093/jn/116.10.1873 10.3390/ani9090652 10.2527/jas1984.593823x 10.1186/s13059-014-0550-8 10.1186/1471-2105-12-328 10.1111/j.1365-2672.1991.tb02932.x 10.1016/j.jare.2018.02.005 10.1139/m87-041 10.1007/s12011-018-1529-1 10.1007/s10661-016-5146-1 10.1007/978-1-4615-1777-1_12 10.1093/bioinformatics/btu638 10.1201/9781351077385-5 |
ContentType | Journal Article |
Copyright | Copyright © 2020 Lu, Xu, Kong, Shen and Aschenbach. Copyright © 2020 Lu, Xu, Kong, Shen and Aschenbach. 2020 Lu, Xu, Kong, Shen and Aschenbach |
Copyright_xml | – notice: Copyright © 2020 Lu, Xu, Kong, Shen and Aschenbach. – notice: Copyright © 2020 Lu, Xu, Kong, Shen and Aschenbach. 2020 Lu, Xu, Kong, Shen and Aschenbach |
DBID | NPM AAYXX CITATION 7X8 5PM DOA |
DOI | 10.3389/fmicb.2020.596681 |
DatabaseName | PubMed CrossRef MEDLINE - Academic PubMed Central (Full Participant titles) DOAJ Directory of Open Access Journals |
DatabaseTitle | PubMed CrossRef MEDLINE - Academic |
DatabaseTitleList | PubMed CrossRef |
Database_xml | – sequence: 1 dbid: DOA name: DOAJ Directory of Open Access Journals url: https://www.doaj.org/ sourceTypes: Open Website – sequence: 2 dbid: NPM name: PubMed url: https://proxy.k.utb.cz/login?url=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database |
DeliveryMethod | fulltext_linktorsrc |
Discipline | Biology |
EISSN | 1664-302X |
EndPage | 596681 |
ExternalDocumentID | oai_doaj_org_article_61366dd0a0804eef88a4245b8581fa91 10_3389_fmicb_2020_596681 33414773 |
Genre | Journal Article |
GrantInformation_xml | – fundername: Natural Science Foundation of Jiangsu Province – fundername: National Natural Science Foundation of China |
GroupedDBID | 53G 5VS 9T4 AAFWJ AAKDD ACGFO ACGFS ACXDI ADBBV ADRAZ AENEX AFPKN ALMA_UNASSIGNED_HOLDINGS AOIJS BAWUL BCNDV DIK ECGQY GROUPED_DOAJ GX1 HYE IAO IEA IHR IPNFZ KQ8 M48 M~E NPM O5R O5S OK1 PGMZT RIG RNS RPM AAYXX CITATION 7X8 ITC 5PM |
ID | FETCH-LOGICAL-c465t-f9665baf1ae943bc1e7e73cabfc70199f85808b9b34d174ea962e831185e3e983 |
IEDL.DBID | RPM |
ISSN | 1664-302X |
IngestDate | Fri Oct 04 13:10:39 EDT 2024 Tue Sep 17 21:11:51 EDT 2024 Fri Aug 16 21:59:47 EDT 2024 Thu Sep 26 20:03:04 EDT 2024 Sat Sep 28 08:45:44 EDT 2024 |
IsDoiOpenAccess | true |
IsOpenAccess | true |
IsPeerReviewed | true |
IsScholarly | true |
Keywords | functional changes ruminal microbiome Ni-dependent enzyme rumen urea supplementation |
Language | English |
License | Copyright © 2020 Lu, Xu, Kong, Shen and Aschenbach. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
LinkModel | DirectLink |
MergedId | FETCHMERGED-LOGICAL-c465t-f9665baf1ae943bc1e7e73cabfc70199f85808b9b34d174ea962e831185e3e983 |
Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by: Emilio M. Ungerfeld, Institute of Agricultural Research (INIA), Chile This article was submitted to Systems Microbiology, a section of the journal Frontiers in Microbiology Reviewed by: Hilario C. Mantovani, Universidade Federal de Viçosa, Brazil; Robert Hausinger, Michigan State University, United States; Rosalind Ann Gilbert, Department of Agriculture and Fisheries, Queensland Government, Australia |
OpenAccessLink | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7782429/ |
PMID | 33414773 |
PQID | 2476566844 |
PQPubID | 23479 |
PageCount | 1 |
ParticipantIDs | doaj_primary_oai_doaj_org_article_61366dd0a0804eef88a4245b8581fa91 pubmedcentral_primary_oai_pubmedcentral_nih_gov_7782429 proquest_miscellaneous_2476566844 crossref_primary_10_3389_fmicb_2020_596681 pubmed_primary_33414773 |
PublicationCentury | 2000 |
PublicationDate | 2020-12-22 |
PublicationDateYYYYMMDD | 2020-12-22 |
PublicationDate_xml | – month: 12 year: 2020 text: 2020-12-22 day: 22 |
PublicationDecade | 2020 |
PublicationPlace | Switzerland |
PublicationPlace_xml | – name: Switzerland |
PublicationTitle | Frontiers in microbiology |
PublicationTitleAlternate | Front Microbiol |
PublicationYear | 2020 |
Publisher | Frontiers Media S.A |
Publisher_xml | – name: Frontiers Media S.A |
References | Ragsdale (B46) 2007; 101 Jin (B20) 2017; 8 Han (B15) 2015; 10 Spears (B55) 1980 Guindon (B14) 2010; 59 Sunderman (B57) 1993; 19 Owens (B39) 1980; 50 Suttisansanee (B58) 2011; 286 Immig (B18) 1996; 42 Wozny (B62) 1977; 33 Langmead (B22) 2012; 9 Spears (B51) 1984; 59 Franzolin (B11) 2012; 64 Spears (B53) 1986; 116 Patra (B43) 2019; 10 Taylor-Edwards (B59) 2009; 87 Ceconi (B6) 2015; 93 Aschenbach (B4) 2011; 89 Immig (B19) 1996; 49 Ludden (B24) 2000; 78 Zoetendal (B66) 1998; 64 Marounek (B27) 1986; 61 Patra (B42) 2018; 13 Parks (B40) 2015; 25 Alneberg (B1) 2014; 11 Boer (B5) 2014; 544 Xu (B63) 2019; 9 McDonald (B28) 1975 Zhou (B65) 2017; 101 Mackie (B25) 1994 Miron (B31) 1991; 70 Anders (B2) 2015; 31 Maroney (B26) 2014; 114 Paul (B44) 2017; 97 Ernst (B9) 2005; 73 Farmer (B10) 2004; 82 Anke (B3) 1977; 27 Gordon (B13) 2010 Kudo (B21) 1987; 33 Han (B16) 1988 Spears (B56) 1977; 60 Spears (B54) 1978; 47 Schmieder (B49) 2011; 6 Van Soest (B60) 1991; 74 McMurdie (B29) 2013; 8 Nolan (B34) 2002; 70 Oscar (B38) 1987; 64 Spears (B52) 2019; 188 Love (B23) 2014; 15 Oscar (B37) 1988; 66 Oksanen (B36) 2016 Peng (B45) 2012; 28 Fu (B12) 2014; 16 Rahnama (B47) 2016; 188 Yang (B64) 2012; 90 Moriya (B32) 2007; 35 Singh (B50) 2019; 190 Whitford (B61) 2001; 1 Rho (B48) 2010; 38 Edgar (B8) 2004; 32 O’Dell (B35) 1971; 32 Parks (B41) 2011; 12 Henderson (B17) 2016; 6 Cunniff (B7) 1997 Milne (B30) 1990; 50 Mulrooney (B33) 2003; 27 |
References_xml | – year: 1997 ident: B7 publication-title: Official Methods of Analysis of AOAC International. contributor: fullname: Cunniff – volume: 49 start-page: 363 year: 1996 ident: B19 article-title: Attempts to induce reductive acetogenesis into a sheep rumen. publication-title: Arch. Tierernahr. doi: 10.1080/17450399609381898 contributor: fullname: Immig – volume: 78 start-page: 188 year: 2000 ident: B24 article-title: Influence of the novel urease inhibitor N-(n-butyl) thiophosphoric triamide on ruminant nitrogen metabolism: II. Ruminal nitrogen metabolism, diet digestibility, and nitrogen balance in lambs. publication-title: J. Anim. Sci. doi: 10.2527/2000.781188x contributor: fullname: Ludden – volume: 73 start-page: 7252 year: 2005 ident: B9 article-title: The nickel-responsive regulator NikR controls activation and repression of gene transcription in Helicobacter pylori. publication-title: Infect. Immun. doi: 10.1128/iai.73.11.7252-7258.2005 contributor: fullname: Ernst – volume: 6 year: 2011 ident: B49 article-title: Fast identification and removal of sequence contamination from genomic and metagenomic datasets. publication-title: PLoS One doi: 10.1371/journal.pone.0017288 contributor: fullname: Schmieder – volume: 101 start-page: 6205 year: 2017 ident: B65 article-title: Effect of urea-supplemented diets on the ruminal bacterial and archaeal community composition of finishing bulls. publication-title: Appl. Microbiol. Biotechnol. doi: 10.1007/s00253-017-8323-4 contributor: fullname: Zhou – volume: 60 start-page: 1073 year: 1977 ident: B56 article-title: Rumen bacterial urease requirement for nickel. publication-title: J. Dairy Sci. doi: 10.3168/jds.s0022-0302(77)83990-8 contributor: fullname: Spears – volume: 61 start-page: 81 year: 1986 ident: B27 article-title: Stoichiometry of glucose and starch splitting by strains of amylolytic bacteria from the rumen and anaerobic digester. publication-title: J. Appl. Bacteriol. doi: 10.1111/j.1365-2672.1986.tb03761.x contributor: fullname: Marounek – volume: 11 start-page: 1144 year: 2014 ident: B1 article-title: Binning metagenomic contigs by coverage and composition. publication-title: Nat. Methods doi: 10.1038/nmeth.3103 contributor: fullname: Alneberg – year: 2016 ident: B36 publication-title: vegan: Community Ecology Package, v.2.3-5. contributor: fullname: Oksanen – year: 1975 ident: B28 article-title: Digestion and metabolism in the ruminant publication-title: Proceedings of the IV International Symposium on Ruminant Physiology contributor: fullname: McDonald – volume: 93 start-page: 357 year: 2015 ident: B6 article-title: Effect of urea inclusion in diets containing corn dried distillers grains on feedlot cattle performance, carcass characteristics, ruminal fermentation, total tract digestibility, and purine derivatives-to-creatinine index. publication-title: J. Anim. Sci. doi: 10.2527/jas.2014-8214 contributor: fullname: Ceconi – volume: 286 start-page: 38367 year: 2011 ident: B58 article-title: Structural variation in bacterial glyoxalase I enzymes: investigation of the metalloenzyme glyoxalase I from Clostridium acetobutylicum. publication-title: J. Biol. Chem. doi: 10.1074/jbc.m111.251603 contributor: fullname: Suttisansanee – volume: 33 start-page: 1097 year: 1977 ident: B62 article-title: Urease assay and urease-producing species of anaerobes in the bovine rumen and human feces. publication-title: Appl. Environ. Microbiol. doi: 10.1128/aem.33.5.1097-1104.1977 contributor: fullname: Wozny – volume: 64 start-page: 131 year: 2012 ident: B11 article-title: Analysis of rumen methanogen diversity in water buffaloes (Bubalus bubalis) under three different diets. publication-title: Microb. Ecol. doi: 10.1007/s00248-012-0007-0 contributor: fullname: Franzolin – volume: 32 start-page: 1792 year: 2004 ident: B8 article-title: MUSCLE: multiple sequence alignment with high accuracy and high throughput. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkh340 contributor: fullname: Edgar – volume: 32 start-page: 769 year: 1971 ident: B35 article-title: Effect of dietary nickel level on excretion and nickel content of tissues in male calves. publication-title: J. Anim. Sci. doi: 10.2527/jas1971.324769x contributor: fullname: O’Dell – volume: 42 start-page: 57 year: 1996 ident: B18 article-title: The rumen and hindgut as source of ruminant methanogenesis. publication-title: Environ. Monit. Assess. doi: 10.1007/bf00394042 contributor: fullname: Immig – volume: 66 start-page: 2313 year: 1988 ident: B37 article-title: Nickel-induced alterations of in vitro and in vivo ruminal fermentation. publication-title: J. Anim. Sci. doi: 10.2527/jas1988.6692313x contributor: fullname: Oscar – volume: 87 start-page: 200 year: 2009 ident: B59 article-title: Effects of slow-release urea on ruminal digesta characteristics and growth performance in beef steers. publication-title: J. Anim. Sci. doi: 10.2527/jas.2008-0912 contributor: fullname: Taylor-Edwards – volume: 16 start-page: 3181 year: 2014 ident: B12 article-title: Evidence for function overlapping of CymA and the cytochrome bc1 complex in the Shewanella oneidensis nitrate and nitrite respiration. publication-title: Environ. Microbiol. doi: 10.1111/1462-2920.12457 contributor: fullname: Fu – volume: 10 year: 2015 ident: B15 article-title: Rumen bacterial diversity of 80 to 110-day-old goats using 16S rRNA sequencing. publication-title: PLoS One doi: 10.1371/journal.pone.0117811 contributor: fullname: Han – year: 1988 ident: B16 publication-title: Digestion and Metabolism of Rumen in Ruminants. contributor: fullname: Han – volume: 9 start-page: 357 year: 2012 ident: B22 article-title: Fast gapped-read alignment with Bowtie 2. publication-title: Nat. Methods doi: 10.1038/nmeth.1923 contributor: fullname: Langmead – volume: 544 start-page: 142 year: 2014 ident: B5 article-title: Nickel-dependent metalloenzymes. publication-title: Arch. Biochem. Biophys. doi: 10.1016/j.abb.2013.09.002 contributor: fullname: Boer – volume: 82 start-page: 884 year: 2004 ident: B10 article-title: Effect of supplementation frequency and supplemental urea level on dormant tallgrass-prairie hay intake and digestion by beef steers and prepartum performance of beef cows grazing dormant tallgrass-prairie. publication-title: J. Anim. Sci. doi: 10.1093/ansci/82.3.884 contributor: fullname: Farmer – volume: 50 start-page: 527 year: 1980 ident: B39 article-title: Slow ammonia release from urea: rumen and metabolism studies. publication-title: J. Anim. Sci. doi: 10.2527/jas1980.503527x contributor: fullname: Owens – volume: 101 start-page: 1657 year: 2007 ident: B46 article-title: Nickel and the carbon cycle. publication-title: J. Inorg. Biochem. doi: 10.1016/j.jinorgbio.2007.07.014 contributor: fullname: Ragsdale – volume: 10 year: 2019 ident: B43 article-title: Dietary bioactive lipid compounds rich in menthol alter interactions among members of Ruminal microbiota in sheep. publication-title: Front. Microbiol. doi: 10.3389/fmicb.2019.02038 contributor: fullname: Patra – volume: 190 start-page: 65 year: 2019 ident: B50 article-title: Effects of nickel supplementation on antioxidant status, immune characteristics, and energy and lipid metabolism in growing cattle. publication-title: Biol. Trace Elem. Res. doi: 10.1007/s12011-018-1524-6 contributor: fullname: Singh – volume: 47 start-page: 1345 year: 1978 ident: B54 article-title: Nickel for ruminants I. Influence of dietary nickel on ruminal urease activity. publication-title: J. Anim. Sci. doi: 10.2527/jas1978.4761345x contributor: fullname: Spears – volume: 25 start-page: 1043 year: 2015 ident: B40 article-title: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. publication-title: Genome Res. doi: 10.1101/gr.186072.114 contributor: fullname: Parks – volume: 64 start-page: 3854 year: 1998 ident: B66 article-title: Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. publication-title: Appl. Environ. Microbiol. doi: 10.1128/aem.64.10.3854-3859.1998 contributor: fullname: Zoetendal – volume: 27 start-page: 25 year: 1977 ident: B3 article-title: Nickel-an essential trace element. 1. Influence of the supply of nickel on live weight gains, food consumption and body composition of growing pigs and goats. publication-title: Arch. Tierernahr. doi: 10.1080/17450397709440608 contributor: fullname: Anke – volume: 1 year: 2001 ident: B61 article-title: Phylogenetic analysis of methanogens from the bovine rumen. publication-title: BMC Microbiol. doi: 10.1186/1471-2180-1-5 contributor: fullname: Whitford – volume: 8 year: 2017 ident: B20 article-title: Differences in ureolytic bacterial composition between the rumen digesta and rumen wall based on ureC gene classification. publication-title: Front. Microbiol. doi: 10.3389/fmicb.2017.00385 contributor: fullname: Jin – volume: 6 year: 2016 ident: B17 article-title: Erratum: rumen microbial community composition varies with diet and host, but a core microbiome is found across a wide geographical range. publication-title: Sci. Rep. doi: 10.1038/srep19175 contributor: fullname: Henderson – volume: 74 start-page: 3583 year: 1991 ident: B60 article-title: Methods for dietary fiber, neutral detergent fiber, and nonstarch polysaccharides in relation to animal nutrition. publication-title: J. Dairy Sci. doi: 10.3168/jds.s0022-0302(91)78551-2 contributor: fullname: Van Soest – volume: 28 start-page: 1420 year: 2012 ident: B45 article-title: IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. publication-title: Bioinformatics doi: 10.1093/bioinformatics/bts174 contributor: fullname: Peng – volume: 59 start-page: 307 year: 2010 ident: B14 article-title: New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. publication-title: Syst. Biol. doi: 10.1093/sysbio/syq010 contributor: fullname: Guindon – volume: 70 start-page: 685 year: 2002 ident: B34 article-title: In vivo behavior of a Helicobacter pylori SS1 nixA mutant with reduced urease activity. publication-title: Infect. Immun. doi: 10.1128/iai.70.2.685-691.2002 contributor: fullname: Nolan – volume: 90 start-page: 307 year: 2012 ident: B64 article-title: An energy-rich diet enhances expression of Na(+)/H(+) exchanger isoform 1 and 3 messenger RNA in rumen epithelium of goat. publication-title: J. Anim. Sci. doi: 10.2527/jas.2011-3854 contributor: fullname: Yang – volume: 27 start-page: 239 year: 2003 ident: B33 article-title: Nickel uptake and utilization by microorganisms. publication-title: FEMS Microbiol. Rev. doi: 10.1016/s0168-6445(03)00042-1 contributor: fullname: Mulrooney – volume: 38 year: 2010 ident: B48 article-title: FragGeneScan: predicting genes in short and error-prone reads. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkq747 contributor: fullname: Rho – year: 2010 ident: B13 publication-title: FASTX-Toolkit. FASTQ/A short-reads pre-processing tools (unpublished). contributor: fullname: Gordon – volume: 35 start-page: W182 year: 2007 ident: B32 article-title: KAAS: an automatic genome annotation and pathway reconstruction server. publication-title: Nucleic Acids Res. doi: 10.1093/nar/gkm321 contributor: fullname: Moriya – volume: 50 start-page: 507 year: 1990 ident: B30 article-title: The effect of supplementary nickel on urea metabolism in sheep given a low protein diet. publication-title: Anim. Sci. doi: 10.1017/s0003356100004992 contributor: fullname: Milne – volume: 89 start-page: 1092 year: 2011 ident: B4 article-title: Ruminant nutrition symposium: role of fermentation acid absorption in the regulation of ruminal pH. publication-title: J. Anim. Sci. doi: 10.2527/jas.2010-3301 contributor: fullname: Aschenbach – volume: 114 start-page: 4206 year: 2014 ident: B26 article-title: Nonredox nickel enzymes. publication-title: Chem. Rev. doi: 10.1021/cr4004488 contributor: fullname: Maroney – volume: 8 year: 2013 ident: B29 article-title: phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. publication-title: PLoS One doi: 10.1371/journal.pone.0061217 contributor: fullname: McMurdie – volume: 64 start-page: 887 year: 1987 ident: B38 article-title: Performance, methanogenesis and nitrogen metabolism of finishing steers fed monensin and nickel. publication-title: J. Anim. Sci. doi: 10.2527/jas1987.643887x contributor: fullname: Oscar – volume: 97 start-page: 3284 year: 2017 ident: B44 article-title: Comparative community structure of archaea in rumen of buffaloes and cattle. publication-title: J. Sci. Food Agric. doi: 10.1002/jsfa.8177 contributor: fullname: Paul – volume: 116 start-page: 1873 year: 1986 ident: B53 article-title: Effects of dietary nickel and protein on growth, nitrogen metabolism and tissue concentrations of nickel, iron, zinc, manganese and copper in calves. publication-title: J. Nutr. doi: 10.1093/jn/116.10.1873 contributor: fullname: Spears – volume: 9 year: 2019 ident: B63 article-title: Effects of incremental urea supplementation on rumen fermentation, nutrient digestion, plasma metabolites, and growth performance in fattening lambs. publication-title: Animals (Basel) doi: 10.3390/ani9090652 contributor: fullname: Xu – volume: 59 start-page: 823 year: 1984 ident: B51 article-title: Nickel as a “Newer Trace Element” in the nutrition of domestic animals. publication-title: J. Anim. Sci. doi: 10.2527/jas1984.593823x contributor: fullname: Spears – volume: 15 year: 2014 ident: B23 article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. publication-title: Genome Biol. doi: 10.1186/s13059-014-0550-8 contributor: fullname: Love – volume: 12 year: 2011 ident: B41 article-title: Classifying short genomic fragments from novel lineages using composition and homology. publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-12-328 contributor: fullname: Parks – volume: 70 start-page: 245 year: 1991 ident: B31 article-title: The hydrolysis of lucerne cell-wall monosaccharide components by monocultures or pair combinations of defined ruminal bacteria. publication-title: J. Appl. Bacteriol. doi: 10.1111/j.1365-2672.1991.tb02932.x contributor: fullname: Miron – volume: 13 start-page: 39 year: 2018 ident: B42 article-title: Ureases in the gastrointestinal tracts of ruminant and monogastric animals and their implication in urea-N/ammonia metabolism: a review. publication-title: J. Adv. Res. doi: 10.1016/j.jare.2018.02.005 contributor: fullname: Patra – volume: 33 start-page: 244 year: 1987 ident: B21 article-title: Interactions between Treponema bryantii and cellulolytic bacteria in the in vitro degradation of straw cellulose. publication-title: Can. J. Microbiol. doi: 10.1139/m87-041 contributor: fullname: Kudo – volume: 188 start-page: 35 year: 2019 ident: B52 article-title: Boron, chromium, manganese, and nickel in agricultural animal production. publication-title: Biol. Trace Elem. Res. doi: 10.1007/s12011-018-1529-1 contributor: fullname: Spears – volume: 188 year: 2016 ident: B47 article-title: The use of rapidly synergistic cloud point extraction for the separation and preconcentration of trace amounts of Ni (II) ions from food and water samples coupling with flame atomic absorption spectrometry determination. publication-title: Environ. Monit. Assess. doi: 10.1007/s10661-016-5146-1 contributor: fullname: Rahnama – year: 1980 ident: B55 publication-title: Role of Nickel in Ruminant Nutrition. contributor: fullname: Spears – start-page: 331 year: 1994 ident: B25 publication-title: Acetogenesis and the Rumen: Syntrophic Relationships, Drake., H.L. doi: 10.1007/978-1-4615-1777-1_12 contributor: fullname: Mackie – volume: 31 start-page: 166 year: 2015 ident: B2 article-title: HTSeq-a Python framework to work with high-throughput sequencing data. publication-title: Bioinformatics doi: 10.1093/bioinformatics/btu638 contributor: fullname: Anders – volume: 19 start-page: 34 year: 1993 ident: B57 article-title: Biological monitoring of nickel in humans. publication-title: Scand. J. Work Environ. Health doi: 10.1201/9781351077385-5 contributor: fullname: Sunderman |
SSID | ssj0000402000 |
Score | 2.3316557 |
Snippet | Urea is an inexpensive non-protein nitrogen source commonly supplemented to the diets of ruminants. It is cleaved to ammonia by bacterial ureases, which... |
SourceID | doaj pubmedcentral proquest crossref pubmed |
SourceType | Open Website Open Access Repository Aggregation Database Index Database |
StartPage | 596681 |
SubjectTerms | functional changes Microbiology Ni-dependent enzyme rumen ruminal microbiome urea supplementation |
SummonAdditionalLinks | – databaseName: DOAJ Directory of Open Access Journals dbid: DOA link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Nb9QwELVQJSQuCMrXAq2MxAnJkMR2bB8L7apCag-IFb1ZjjNRcyBbdbOH5Zfwc5mxs9VuhcSFaxI51rxJ5j2PPcPYewrpdVRROFkEoVrQwoLqBKgAGkOCk2kx5-KyPl-or1f6aqfVF-0Jy-WBs-E-Ybip67YtAlIbBdBZGyhZ11htyy64LHxKvSOm0j-YZFExpTFRhTmEqY8N6sGq-KiR4ttyLxClev1_I5n390ruBJ_5E_Z4Yo38JM_2KXsAwyF7mPtIbp6x33OMTnlRj-fjAiu-7DhyOz4dABk3dOGCdt81ePNHP17zy16cTi1wR342_Nr8BE5VqFecWkik3wQ_acNNTtZvB_y2Tm3AprHo8D4fl3yB3FOkDqFpuRFaftrDuHrOFvOz71_OxdRyQURV61F0aBrdhK4M4JRsYgkGjIyh6SLVbXcdmr2wjWukalHLQHB1BVaiStEgwVn5gh0MywFeMV5rh1CbFhVkVK2ROESholOxgo5yvTP2YWt_f5Mra3hUJASWT2B5AstnsGbsMyF09yAVxU4X0FX85Cr-X64yY--2-Hr8iCgzEgZYrle-UoZ4rVU4q5cZ77tXSYzzyhg5Y2bPE_bmsn9n6K9ToW6D9Att8Pp_TP4Ne0T2oJ00VfWWHYy3azhCPjQ2x8n1_wAm8woX priority: 102 providerName: Directory of Open Access Journals – databaseName: Scholars Portal Journals: Open Access dbid: M48 link: http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwrV1Nb9QwELWqVkhcEOVzgSIjcUJKlY3txD4g1NKuKqTtAbGit8h2xjRSScomK7H8En4uM062YtEeucaJY82zPW88nhnG3pJKz730iRGpTWQFKtEgQwLSgkKVYEQ8zJlf5hcL-elKXe2xTXmrUYDdTtOO6kktljfHP3-sP-CCf08WJ-pbRKD2Dk29LD1WyN4pEPsgk0LShJ-PbD9uzGQrpaNvc_eXW9opJvHfxTz_vUD5l0aaPWQPRirJTwbsD9keNI_YvaG45Pox-z1DlTWc9PEhhqDjbeBI-PgYFdKv6cGcruQ5bPxa99f8sk7Oxrq4PT9vfq2_A6fU1B2nuhJx7-Anlb0dPPibDj-vYm2wsS-K6Od9yxdISJNYNjSeQULFz2rouydsMTv_8vEiGeswJF7mqk8CikY5G6YWjBTOT6GAQnjrgqdk7iZopVPtjBOyQgMHrMkz0AJNFwUCjBZP2X7TNvCc8VwZxL-o0Kz0sioEdpFKb6TPIJADeMLebeRf3g7pNko0UwisMoJVEljlANaEnRJCdy9Spuz4oF1-K8eFVyJdyfOqSi1SYwkQtLbk7HU45mmwBjt5s8G3xJVF7hLbQLvqykwWRHa1xFE9G_C--5VA5S-LQkxYsTUTtsay3dLU1zF7d4GcDGXw4n8M_iW7T_Kg6zVZ9ort98sVHCFJ6t3rOPX_ABLSEr8 priority: 102 providerName: Scholars Portal |
Title | Functional Changes of the Community of Microbes With Ni-Dependent Enzyme Genes Accompany Adaptation of the Ruminal Microbiome to Urea-Supplemented Diets |
URI | https://www.ncbi.nlm.nih.gov/pubmed/33414773 https://search.proquest.com/docview/2476566844 https://pubmed.ncbi.nlm.nih.gov/PMC7782429 https://doaj.org/article/61366dd0a0804eef88a4245b8581fa91 |
Volume | 11 |
hasFullText | 1 |
inHoldings | 1 |
isFullTextHit | |
isPrint | |
link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3da9swEBdtYbCXse9lH0WDPQ2cOJZkSY9d26wMUsZYWN6MJJ9WQ2OHxnnI_pL-uT3JdmnGnvbiB9u5CP3Out_pTneEfAomPXfcJZqlJuEliEQB9wlwAwJNgmZxM2d-mV8s-LelWB4QMZyFiUn7zlbj-no1rqurmFu5XrnJkCc2-T4_lWjWUMzkkBxKxh646HH5DR5R2kcw0QHTiFDlLLqCWToWyO5V6A7DcPXmUrI9cxSr9v-Lav6dMfnABM2ekic9d6Qn3RifkQOon5NHXTfJ3QtyO0Mb1W3t0e7QwIY2niLDo_0xkHYXbsxDDp7Fh7-q9opeVslZ3wi3pef1n90KaKhFvaGhkURcLOhJadZdyH4Q-GMbm4H1ssIRfto2dIEMNIl9QuOmI5T0rIJ285IsZuc_Ty-SvvFC4ngu2sTjLAlr_NSA5sy6KUiQzBnrXajerr0SKlVWW8ZL9GjA6DwDxdBXEcBAK_aKHNVNDW8IzYVGpGSJfqTjpWQoIuVOc5eBDxHfEfk8zH-x7uprFOiXBNyKiFsRcCs63EbkS0Do_sVQGjveaG5-F72CFMhP8rwsU4NcmAN4pUyI7loc89QbjUI-DvgW-CmF-IipodluiozLwG4Vx1G97vC-_6tBX0ZE7mnC3lj2n6D2xnLdvba-_e9fviOPwySEJJose0-O2pstfEAq1NrjuIWA16_LKV7nXB3Hj-EOK6UOAA |
link.rule.ids | 230,315,733,786,790,870,891,2115,24346,27955,27956,53825,53827 |
linkProvider | National Library of Medicine |
linkToHtml | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9QwELZKEYIL78fyNBInpGSzsZ3Ex9J2tUB3hVAXerNsZ0KjdpNVN3vY_hJ-LmMnqboVF7jaycSxP3u-scczhHxwKj2x3AaSRTrgOYggA14EwDUIVAmS-c2c6SyZzPmXE3GyQ0R_F8Y77VtThtX5IqzKU-9buVzYYe8nNvw23U9RraGY4S1yG-drLK4Z6X4BdjZR1J1hogkmcYxKa9AYjKNQIL_PXH4Yhus3T1O2pZB83P6_kc2bPpPXlND4AfnRN7_1PTkL140J7eWNyI7__H8Pyf2OltK9tvoR2YHqMbnTJqrcPCG_x6j-2l1D2t5HWNG6oEgeaXfDpNm4gqlz7zNY-bNsTumsDA66HLsNPawuNwugLsz1irocFX4donu5XrbeAL3A72ufZ6yT5aID0KamcyS3gU9B6vczIacHJTSrp2Q-PjzenwRdTofA8kQ0QYHdL4wuRhokZ8aOIIWUWW0K6wLDyyITWZQZaRjP0VgCLZMYMoZmkAAGMmPPyG5VV_CC0ERI7KQ0RxPV8jxlKCLiVnIbQ-EOkwfkYz-watmG7lBo8jhAKA8I5QChWkAMyCc39FcPuqjbvqC--KW6sVFIfZIkzyONNJsDFFmm3cGxwTaPCi1RyPseOApnqTt60RXU65WKeeqIc8axVc9bIF19qgfigKRbENtqy3YNAsdHAu-A8vK_33xH7k6Op0fq6PPs6ytyz3WI89WJ49dkt7lYwxtkXI156-fXH4ziLT0 |
linkToPdf | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV1Lb9swDBa2Dht22fuRPTVgpwF2HEu2rGPXNOgeCYphwYpdBEmmV6ONHTTOIf0l-7mjZLtIip16tWxaNj-JHyWKJOSjM-mp5TaQLNIBzyEJMuBFAFxDgiZBMr-YM52lR3P-9SQ52Sr15YP2rSnD6nwRVuWpj61cLuywjxMbHk8PBJo1FDNc5sXwNrmDYzYWW466n4SdXxR1-5johknUU2kNOoRxFCbI8TNXI4bhHM6FYDtGyefu_x_hvB43uWWIJg_J7_4T2viTs3DdmNBeXsvueKNvfEQedPSU7re3PCa3oHpC7rYFKzdPyd8JmsF29ZC25xJWtC4okkjanTRpNu7C1IX5GWz8VTandFYG467WbkMPq8vNAqhLd72irlaFn4_ofq6XbVRAL_DH2tcb62S5LAG0qekcSW7gS5H6dU3I6biEZvWMzCeHPw-Ogq62Q2B5mjRBgSpIjC5GGiRnxo5AgGBWm8K6BPGyyJIsyow0jOfoNIGWaQwZQ3coAQYyY8_JXlVX8JLQNJH4o0SOrqrluWAoIuJWchtD4TaVB-RTr1y1bFN4KHR9HCiUB4VyoFAtKAbks1P_1Y0u-7a_UF_8UZ1-FFKgNM3zSCPd5gBFlmm3gWywz6NCSxTyoQePwtHqtmB0BfV6pWIuHIHOOPbqRQumq1f1YBwQsQOznb7stiB4fEbwDiyvbvzke3LveDxR37_Mvr0m993_cCE7cfyG7DUXa3iLxKsx7_wQ-wffAi-9 |
openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Functional+Changes+of+the+Community+of+Microbes+With+Ni-Dependent+Enzyme+Genes+Accompany+Adaptation+of+the+Ruminal+Microbiome+to+Urea-Supplemented+Diets&rft.jtitle=Frontiers+in+microbiology&rft.au=Zhongyan+Lu&rft.au=Zhihui+Xu&rft.au=Zhihui+Xu&rft.au=Lingmeng+Kong&rft.date=2020-12-22&rft.pub=Frontiers+Media+S.A&rft.eissn=1664-302X&rft.volume=11&rft_id=info:doi/10.3389%2Ffmicb.2020.596681&rft.externalDBID=DOA&rft.externalDocID=oai_doaj_org_article_61366dd0a0804eef88a4245b8581fa91 |
thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=1664-302X&client=summon |
thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=1664-302X&client=summon |
thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=1664-302X&client=summon |