Heterogeneous development of methanogens and the correlation with bacteria in the rumen and cecum of sika deer (Cervus nippon) during early life suggest different ecology relevance.

Publisher: BioMed Central Country of Publication: England NLM ID: 100966981 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2180 (Electronic) Linking ISSN: 14712180 NLM ISO Abbreviation: BMC Microbiol Subsets: MEDLINE

Original Publication: London : BioMed Central, [2001-

Bacteria/*classification ; Cecum/*microbiology ; Deer/*growth & development ; High-Throughput Nucleotide Sequencing/*methods ; Rumen/*microbiology; Age Factors ; Anaerobiosis ; Animals ; Bacteria/genetics ; Bacteria/isolation & purification ; Bacteria/metabolism ; Deer/microbiology ; Methane/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA

Background: Enteric methane from the ruminant livestock is a significant source in global greenhouse gas emissions, which is mainly generated by the methanogens inhabiting the rumen and cecum. Sika deer (Cervus nippon) not only produces less methane than bovine, but they also harbor a distinct methanogen community. Whereas, knowledge of methanogens colonization in the rumen and cecum of sika deer is relatively still unknown, which could provide more insights to the manipulation of gut microbiota during early life.
Results: Here, we examined the development of bacteria and methanogens in the rumen and cecum of juvenile sika deer from birth to post-weaning (1 day, 42 days and 70 days, respectively) based on next generation sequencing. The results showed that the facultative anaerobic bacteria were decreased and the cellulolytic bacteria were increased. However, methanogens established soon after birth thrived through the whole developmental period, indicating a different succession process than bacteria in the GIT, and the limited role of age and dietary change on GIT methanogens. We also found Methanobrevibacter spp. (Mean relative abundance = 44.2%) and Methanocorpusculum spp. (Mean relative abundance = 57.5%) were dominated in the rumen and cecum, respectively. The methanogens also formed specific correlations with bacteria under different niches, suggesting a role of ecology niche on methanogen community.
Conclusions: This study contributes to our knowledge about the microbial succession in GIT of sika deer, that may facilitate the development of targeted strategies to improve GIT function of sika deer.

PeerJ. 2014 Aug 05;2:e494. (PMID: 25165621)
Int J Syst Evol Microbiol. 2016 Feb;66(2):768-773. (PMID: 26619944)
Sci Rep. 2015 Aug 04;5:12693. (PMID: 26239401)
PLoS One. 2013;8(2):e47879. (PMID: 23408926)
ISME J. 2013 Jun;7(6):1069-79. (PMID: 23426008)
Br J Nutr. 1976 Jul;36(1):1-14. (PMID: 949464)
BMC Microbiol. 2013 Sep 12;13:207. (PMID: 24228793)
J Appl Microbiol. 2014 Feb;116(2):245-57. (PMID: 24279326)
Bioinformatics. 2011 Aug 15;27(16):2194-200. (PMID: 21700674)
Nucleic Acids Res. 2013 Jan 7;41(1):e1. (PMID: 22933715)
J Bacteriol. 2012 Dec;194(24):6944-5. (PMID: 23209209)
Bioinformatics. 2011 Feb 1;27(3):431-2. (PMID: 21149340)
PLoS One. 2014 Nov 10;9(11):e112846. (PMID: 25383707)
Curr Opin Infect Dis. 2014 Oct;27(5):459-64. (PMID: 25023740)
Sci Rep. 2015 Oct 09;5:14567. (PMID: 26449758)
PLoS Genet. 2016 Feb 18;12(2):e1005846. (PMID: 26891056)
J Anim Sci Biotechnol. 2017 Jan 19;8:7. (PMID: 28123698)
Front Microbiol. 2017 Feb 07;8:159. (PMID: 28223972)
Sci Total Environ. 2016 Dec 1;572:1166-1174. (PMID: 27519318)
Sci Rep. 2017 Jan 18;7:40864. (PMID: 28098248)
ISME J. 2018 Feb;12(2):411-423. (PMID: 29135970)
Biochem J. 1948;43(1):99-109. (PMID: 16748377)
Sci Total Environ. 2017 Feb 1;579:1572-1580. (PMID: 27923575)
Environ Microbiol. 2012 Jan;14(1):129-39. (PMID: 21906219)
Nat Biotechnol. 2018 Apr;36(4):359-367. (PMID: 29553575)
ISME J. 2017 Sep;11(9):2059-2074. (PMID: 28585938)
Microb Ecol. 2010 Nov;60(4):721-9. (PMID: 20585943)
Nat Methods. 2013 Oct;10(10):996-8. (PMID: 23955772)
FEMS Microbiol Lett. 2019 Feb 1;366(4):. (PMID: 30649337)
FEMS Microbiol Lett. 1995 Dec 1;134(1):45-50. (PMID: 8593954)
Arch Mikrobiol. 1967;59(1):158-64. (PMID: 5628850)
Appl Environ Microbiol. 2013 Mar;79(6):1777-86. (PMID: 23241983)
Front Microbiol. 2015 Apr 10;6:296. (PMID: 25914693)
Archaea. 2005 May;1(5):353-63. (PMID: 15876569)
Front Microbiol. 2015 Oct 14;6:1133. (PMID: 26528276)
Stand Genomic Sci. 2009 Sep 24;1(2):197-203. (PMID: 21304657)
Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6. (PMID: 23193283)
J Anim Sci. 1995 Aug;73(8):2483-92. (PMID: 8567486)
Int J Syst Evol Microbiol. 2008 Jun;58(Pt 6):1393-7. (PMID: 18523184)
J Anim Sci Biotechnol. 2017 Jan 19;8:8. (PMID: 28116074)
PLoS Genet. 2018 Oct 12;14(10):e1007580. (PMID: 30312316)
J Appl Genet. 2015 Aug;56(3):411-26. (PMID: 25663664)
Proc Natl Acad Sci U S A. 2007 Jun 19;104(25):10643-8. (PMID: 17563350)
Gut Microbes. 2014;5(5):628-38. (PMID: 25483332)
Nat Commun. 2013;4:1428. (PMID: 23385573)
Asian-Australas J Anim Sci. 2017 Jul;30(7):967-972. (PMID: 28335097)
Anaerobe. 2004 Oct;10(5):277-85. (PMID: 16701528)
Sci Rep. 2017 Mar 24;7(1):422. (PMID: 28341835)
PLoS One. 2016 May 09;11(5):e0155213. (PMID: 27159387)
J Dairy Sci. 1989 Feb;72(2):485-92. (PMID: 2703570)
PLoS One. 2015 May 08;10(5):e0123481. (PMID: 25955033)
Front Microbiol. 2017 May 24;8:937. (PMID: 28596764)
Front Microbiol. 2018 Jan 23;9:4. (PMID: 29410651)
PLoS One. 2014 Dec 09;9(12):e114513. (PMID: 25490208)
Trends Biotechnol. 2016 Jan;34(1):26-35. (PMID: 26603286)
Trends Mol Med. 2015 Feb;21(2):109-17. (PMID: 25578246)
Appl Microbiol Biotechnol. 2014 Dec;98(23):9749-61. (PMID: 25359471)
BMC Genomics. 2017 Aug 21;18(1):639. (PMID: 28826405)
Genome Biol Evol. 2013;5(10):1769-80. (PMID: 23985970)
Appl Environ Microbiol. 2014 Mar;80(6):2021-8. (PMID: 24441166)
Nat Methods. 2010 May;7(5):335-6. (PMID: 20383131)
J Dairy Sci. 2010 Jul;93(7):3203-15. (PMID: 20630237)
Nat Rev Microbiol. 2008 Feb;6(2):121-31. (PMID: 18180751)
PLoS One. 2015 Jul 17;10(7):e0133048. (PMID: 26186002)
Appl Environ Microbiol. 2004 Apr;70(4):2172-9. (PMID: 15066810)
Front Microbiol. 2017 Aug 15;8:1553. (PMID: 28861065)
Mol Biol Evol. 2009 Jul;26(7):1641-50. (PMID: 19377059)

Keywords: Bacteria; Gastrointestinal tract; Methanogens; Microbiome succession; Regional difference

0 (RNA, Ribosomal, 16S)
OP0UW79H66 (Methane)

Date Created: 20190613 Date Completed: 20200403 Latest Revision: 20200403

20231215

PMC6560721

10.1186/s12866-019-1504-9

31185894