[논문]반추위 마이크로바이옴 내 메탄생성고세균 조사

이슬; 백열창; 이진욱; 김민석

doi:10.5762/kais.2020.21.7.312

[국내논문] 반추위 마이크로바이옴 내 메탄생성고세균 조사
Methanogenic Archaeal Census of Ruminal Microbiomes 원문보기

한국산학기술학회논문지 = Journal of the Korea Academia-Industrial cooperation Society, v.21 no.7, 2020년, pp.312 - 320

이슬 (국립축산과학원 영양생리팀) , 백열창 (국립축산과학원 영양생리팀) , 이진욱 (국립축산과학원 가축유전자원센터) , 김민석 (전남대학교 농업생명과학대학 동물자원학부)

초록
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본 연구의 목적은 Ribosomal Database Project에서 공적으로 활용 가능한 16S rRNA 유전자 시퀀스들의 메타분석을 통해 반추위 고세균의 계통발생 다양성을 조사하는 것이다. 총 8,416개의 시퀀스가 Ribosomal Database Project(출시버전 11, 업데이트 5)로부터 회수되었고, taxonomy tree를 구축하는데 사용되었다. Species 수준의 OTUs가 97% sequence 유사성 기준으로 QIIME 프로그램을 사용하여 분석되었다. 총 8,416개의 시퀀스 중에서 8,412개의 시퀀스는 총 3개의 문으로 분류되었고, 나머지 4개의 시퀀스는 어떤 알려진 문으로 분류되지 못했다. Euryarchaeota는 가장 우점하는 문으로, 전체 고세균 시퀀스의 99.8%를 차지하였다. 이 중에서 차례로 Methanobrevibacter가 65.4%, Methanosphaera가 10.4%, Methanomassillicoccus가 10.4%, Methanomicrobium가 7.9%, Methanobacterium가 1.9%, Methanimicrococcus가 0.5%, Methanosarcina가 0.1%, Methanoculleus가 0.1%를 차지하였다. V2와 V3 영역으로 자른 7,544개의 시퀀스는 493개의 OTUs로 분류되었다. 총 493 OTUs 중에서 단지 17개만 우점하였고, 총 7,544 시퀀스 중 1% 이상을 차지하였다. 본 연구는 반추동물로 부터 메탄발생에 크게 기여하는 반추위 우점 메탄생성균 분석에 대한 향후 연구를 인도하는데 도움을 주고, 사료나 가축품종이 달라져도 이러한 메탄생성균을 억제하는 메탄저감제를 개발하는데 도움을 줄 것이다.

Abstract ▼ AI-Helper

The objective of the study was to undertake a phylogenetic diversity census of ruminal archaea based on a meta-analysis of 16S rRNA gene sequences that were publicly available in the Ribosomal Database Project. A total of 8,416 sequences were retrieved from the Ribosomal Database Project (release 11, update 5) and included in the construction of a taxonomy tree. Species-level operational taxonomic units (OTUs) were analyzed at a 97% sequence similarity by using the QIIME program. Of the 8,416 sequences, 8,412 were classified into one of three phyla; however, the remaining four sequences could not be classified into a known phylum. The Euryarchaeota phylum was predominant and accounted for 99.8% of the archaeal sequences examined. Among the Euryarchaeota, 65.4% were assigned to Methanobrevibacter, followed by Methanosphaera (10.4%), Methanomassillicoccus (10.4%), Methanomicrobium (7.9%), Methanobacterium (1.9%), Methanimicrococcus (0.5%), Methanosarcina (0.1%), and Methanoculleus (0.1%). The 7,544 sequences that had been trimmed to the V2 and V3 regions clustered into 493 OTUs. Only 17 of those 493 OTUs were dominant groups and accounted for more than 1% of the 7,544 sequences. These results can help guide future research into the dominant ruminal methanogens that significantly contribute to methane emissions from ruminants, research that may lead to the development of anti-methanogenic compounds that inhibit these methanogens regardless of diet or animal species.

주제어

표/그림 (2)

그림 Fig. 1. A taxonomic tree showing rumen archaea.
표 Table 1. OTU groups of ruminal archaea

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제안 방법

In conclusion, our study has provided an overview of methanogenic archaea using a meta-analysis of individual studies using Sanger sequencing technology. A collective view of ruminal archaeal communities using a meta-analysis has helped to reduce biased knowledge concerning the structure of ruminal methanogenic archaea.

대상 데이터

[1] examined ruminal archaeal census data using a meta-analysis of ruminal 16S rRNA gene sequences deposited in the RDP database. However, this study used only 3,516 sequences of rumen origin with outdated versions of their taxonomic classifiers.
Of the total 493 OTUs, 12 were not dominant OTU groups but included a sequence (or sequences) recovered from methanogen isolates. These 12 OTUs were assigned to Methanobrevibacter (OTU #22, 113), Methanobacterium (OTU #73, 124, 129, 409), Methanoculleus (OTU #75, 135, 139), Methanosarcina (OTU #63, 132), and Methanomassillicoccus (OTU #375).

성능/효과

The remaining four sequences could not be classified into a known phylum and was assigned to unclassified Archaea. Euryarchaeota was the first predominant phylum and accounted for 8,402 of the 8,412 sequences, whereas phyla Crenarchaeota and Thaumarchaeota were represented by only one and 9 sequences, respectively.
1). Methanobrevibacter and Methanosphaera were the first and the second dominant genera represented by 5,505 and 877 sequences (65.4% and 10.4% of all sequences), respectively. Methanomassillicoccus (873 sequences) belonging to order Thermoplasmatales was represented by 873 sequences (10.
The information on dominant methanogenic taxa with reduced bias may contribute to developing anti-methanogenic compounds exhibiting consistent efficacy irrespective of different breeds, ages, diets, geographic regions, and seasons. Only 0.7% of the total sequences were recovered from cultured methanogens, indicating that additional efforts to isolate new ruminal methanogens are warranted to achieve sustainable methane reduction from ruminant animals.
The first dominant genus, Methanobrevibacter, was represented by nine (OTU #1–3, 6, 7, 11, 14–16) of the 17 dominant OTU groups (Table 1).
The remaining four dominant OTUs (OTU #10, 12, 13, and 17) were assigned to the genus Methanomassillicoccus but were not represented by any isolate sequences. These OTUs were also represented by sequences recovered from the rumen of various animal species, indicating that species corresponding to these four OTUs may play an important role in ruminal methane emissions, irrespective of diet and animal species.
The second dominant genus, Methanosphaera, was represented by two (OTU #4, 8) of the 17 dominant OTU groups but had no sequence recovered from Methanosphaera isolates. OTU #4 was represented by sequences recovered from the rumen of cattle [18-21], muskoxen (unpublished study), sheep [29,30], goats [31], and buffalo (unpublished study), whereas OTU #8 was represented by sequences recovered from the rumen of cattle [20], sika deer [25], reindeer [26], sheep [23], goats (unpublished study), and muskoxen (unpublished study).
The third dominant genus, Methanomicrobium, was represented by one (OTU #5) of the 17 dominant OTU groups and included an isolate sequence recovered from Methanomicrobium mobile. OTU #5 was represented by sequences recovered from the rumen of cattle [21, 28, 32, 33], reindeer [26], yak [28], and muskoxen (unpublished study).

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표제어: PCR

동의어: Packet Collision Rate

용어 설명 출처 목록 (6)

용어 설명: PCR은 세균 특이성이 있는 primer를 이용하여 적은 수의 세균이 있을지라도 쉽게 검출할 수 있는 유용한 방법이며, 이를 이용하여 구강 내 치면세균막이나 타액에서 직접 세균을 검출할 수 있게 되었다[8].

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