search for




 

Draft genome sequence of Anaerostipes faecalis AGMB03513T, an acetate-, propionate-, and butyrate-producing bacterium isolated from swine faeces
Korean J. Microbiol. 2022;58(4):311-313
Published online December 31, 2022
© 2022 The Microbiological Society of Korea.

Seung-Hyeon Choi and Seung-Hwan Park*

Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
Correspondence to: *E-mail: biopark@kribb.re.kr; Tel.: +82-63-570-5636; Fax: +82-63-570-5609
Received August 22, 2022; Revised November 24, 2022; Accepted December 6, 2022.
Abstract
The genus of Anaerostipes is known to have been isolated from the intestines of vertebrates. Likewise, the A. faecalis AGMB03513T was isolated from swine faeces. Whole-genome sequencing of strain AGMB03513T was performed using a NovaSeqTM 6000 System. The draft genome was consisted of 37 contigs with a total length of 2,544,126 bp and a DNA G + C contents of 37.0%. The genome contained 2,446 protein-coding genes, 8 rRNA, 59 tRNA and 72 pseudogenes. In addition, strain AGMB03513T contained genes required for acetate, propionate and butyrate synthesis.
Keywords : Anaerostipes faecalis, draft genome sequence, swine faeces
Body

Short-chain fatty acids (SCFAs), such as acetate, propionate and butyric acid, are end products produced through the fermentation of gut microbiota (Aho et al., 2021). SCFAs maintained intestinal homeostasis by inducing an anti-inflammatory response and enhancing intestinal barrier function (Parada Venegas et al., 2019; Aho et al., 2021). In addition, SCFAs were used as major energy sources for colon cells and affected cell growth, proliferation and differentiation (Liu, 2015; Parada Venegas et al., 2019). Microbial-produced SCFAs increased IgG concentrations and IgA+ cells, reducing the incidence of diarrhea in weaning pigs and improving immune function (Liu, 2015). Moreover, SCFAs increased pig weight gain by helping lipids and carbohydrates metabolism in the pig intestines and improving feed efficiency (Liu, 2015; Zhou et al., 2021).

The genus Anaerostipes was firstly proposed as valid name by Schwiertz et al. (2002), and belonged to the family Lachnospiraceae within the phylum Firmicutes. Currently, the genus Anaerostipes consisted of 8 valid species: A. caccae, A. butyraticus, A. hadrus, A. rhamnosivorans, A. hominis, A. faecis, A, faecalis, and A. amylophilus (https://lpsn.dsmz.de/ genus/anaerostipes). The members of the genus Anaerostipes were isolated from human intestine or faeces, broiler chicken contents, swine faeces and mouse faeces (Choi et al., 2021; Hitch et al., 2021; Lee et al., 2021; Forster et al., 2022). The genus Anaerostipes was strictly anaerobic, rod-shape, non-motile, gram-variable bacteria, which produced butyrate or had related genes (Choi et al., 2021; Hitch et al., 2021; Lee et al., 2021; Forster et al., 2022). Here, we describe the draft genome sequence and annotation of Anaerostipes faecalis AGMB03513T, which we have reported as a novel species.

The strain was cultured using RCM medium (MB cell) in anaerobic chamber (Coy Laboratory Products) containing 90% N2, 5% H2 and 5% CO2. Genomic DNA (gDNA) was extracted using a phenol:chloroform:isoamyl alcohol method (Wilson et al., 1990). The extracted gDNA was measured for quantity and quality with PicoGreen. Then, the extracted gDNA sheared using Covaris LE220 (Covaris). A DNA library was prepared using a TruSeq Nano DNA kit (Illumina). Validation of final product was analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies). Whole-genome sequencing was performed using a NovaSeqTM 6000 System (Illumina) with paired-end read lengths of 151 bp. De novo assembly was performed with the SPAdes version 3.13.0 (Bankevich et al., 2012). Potential contamination of genomic assembly was confirmed by ContEst16S (Lee et al., 2017) and quality was checked by CheckM (Parks et al., 2015). The coding DNA sequences (CDSs) and tRNAs were predicted using Prodigal and tRNAscan-SE, respectively. Genome annotation and analysis were performed using Prodigal, NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (Tatusova et al., 2016) and KEGG (Kanehisa et al., 2014).

The draft genome of A. faecalis AGMB03513T was consisted of 37 contigs with 1306.6× coverage. The length of genome was 2,544,126 bp (N50 value, 232,061 bp) and the DNA G + C content was 37.0%. The NCBI PGAP annotation showed that the genome contains 2,446 protein-coding genes, 8 rRNA, 59 tRNA and 72 pseudogenes (Table 1).

General features of <italic>Anaerostipes faecalis</italic> AGMB03513<sup>T</sup>
Property Value
Genome assembly
Assemble method SPAdes v. 3.13.0
Genome coverage 1306.6×
Genome features
Genome size (bp) 2,544,126
DNA G + C content (%) 37.0
No. of contigs 37
Total genes 2,589
Protein-coding genes 2,446
Complete rRNA genes 1 (5S)
Partial rRNA genes 4, 3 (16S, 23S)
tRNA genes 59
Other RNA 4
Pseudogenes 72
GenBank Accession No. JABRXE000000000


We identified several producible SCFA synthesis pathways in the genome of strain AGMB03513T. Among them, previous studies showed strain AGMB03513T to produces butyrate, acetate and propionate (Choi et al., 2021). First, the genome contained pyruvate ferredoxin oxidoreductase (KTB61_RS05235), acetyl-CoA C-acetyltransferase (KTB61_RS02085), 3-hydroxybutyryl-CoA dehydrogenase (KTB61_RS02095), enoyl-CoA hydratase (KTB61_RS02090) and enoyl-[acyl-carrier protein] reductase (KTB61_RS02260) genes for synthesizing butyrate from pyruvate. Strain AGMB03513T had pyruvate ferredoxin oxidoreductase (KTB61_RS05235), phosphate acetyltransferase (KTB61_RS01375) and acetate kinase (KTB61_RS01380) to produce acetate from pyruvate. Finally, propionate can be synthesized from pyruvate via two pathways. One pathway involved a phosphate acetyltransferase (KTB61_RS01375) and acetate kinase (KTB61_RS01380) genes, and the other involved a l-lactate dehydrogenase (KTB61_RS02120, KTB61_RS02185, KTB61_RS06530) and acetate kinase (KTB61_RS01380) genes.

We performed whole-genome sequencing to understand how strain A. faecalis AGMB03531T produces acetate, propionate and butyrate. These studies suggest that it will help to understand the physiological function of strain AGMB03531T, which synthesizes acetate, propionate and butyrate in the swine gut environment.

Nucleotide sequence accession number

Anaerostipes faecalis AGMB03513T has been deposited in the Korean Collection for Type Cultures under accession number KCTC 25020T. The GenBank/EMBL/DDBJ accession number for the genome sequence of A. faecalis AGMB03513T is JABRXE000000000.

적 요

Anaerostipes 속은 척추동물 내장의 내용물에서 분리된 것으로 알려져 있다. Anaerostipes faecalis AGMB03513T도 돼지 분변에서 분리되었으며, AGMB03513T의 전장 유전체 시퀀싱은 NovaSeq™ 6000 시스템을 이용하여 수행했다. 유전체 초안은 총 길이 2,544,126 bp와 37.0%의 DNA G + C 함량을 갖는 37개의 contig들로 구성되어 있고, 유전체에는 2,446개의 단백질 코딩 유전자, 8개의 rRNA, 59개의 tRNA 그리고 72개의 위유전자를 포함하고 있다. 또한, 균주 AGMB03513T는 아세테이트, 프로피오네이트 및 부틸레이트 합성에 필요한 유전자를 포함한다.

Acknowledgments

This work was supported by the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM5232221). S.-H. P. was supported by the Technology Innovation Program (20009412, Discovery and fermentation optimization of uncultured bacteria from the gut microbiome based on genomic big data), funded by the Ministry of Trade, Industry & Energy (MOTIE, Korea).

Conflict of Interest

The authors have no conflict of interest to report.

References
  1. Aho VTE, Houser MC, Pereira PAB, Chang J, Rudi K, Paulin L, Hertzberg V, Auvinen P, Tansey MG, and Scheperjans F. 2021. Relationships of gut microbiota, short-chain fatty acids, inflammation, and the gut barrier in parkinson's disease. Mol. Neurodegener. 16, 6.
    Pubmed KoreaMed CrossRef
  2. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, and Prjibelski ADPrjibelski AD, et al. 2012. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455-477.
    Pubmed KoreaMed CrossRef
  3. Choi SH, Choi JY, Park JE, Kim JS, Kang SW, Lee J, Lee MK, Lee JS, Lee JH, and Jung HJung H, et al. 2021. Description of Anaerostipes faecalis sp. nov., a new segmented filamentous bacterium isolated from swine faeces. Antonie van Leeuwenhoek 114, 1867-1875.
    Pubmed CrossRef
  4. Forster SC, Clare S, Beresford-Jones BS, Harcourt K, Notley G, Stares MD, Kumar N, Soderholm AT, Adoum A, and Wong HWong H, et al. 2022. Identification of gut microbial species linked with disease variability in a widely used mouse model of colitis. Nat. Microbiol. 7, 590-599.
    Pubmed KoreaMed CrossRef
  5. Hitch TCA, Riedel T, Oren A, Overmann J, Lawley TD, and Clavel T. 2021. Automated analysis of genomic sequences facilitates high-throughput and comprehensive description of bacteria. ISME Commun. 1, 16.
    KoreaMed CrossRef
  6. Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, and Tanabe M. 2014. Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199-D205.
    Pubmed KoreaMed CrossRef
  7. Lee I, Chalita M, Ha SM, Na SI, Yoon SH, and Chun J. 2017. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int. J. Syst. Evol. Microbiol. 67, 2053-2057.
    Pubmed CrossRef
  8. Lee JY, Kang W, Shin NR, Hyun DW, Kim PS, Kim HS, Lee JY, Tak EJ, Sung H, and Bae JW. 2021. Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn's disease. Int. J. Syst. Evol. Microbiol. 71, 005129.
    Pubmed CrossRef
  9. Liu Y. 2015. Fatty acids, inflammation and intestinal health in pigs. J. Anim. Sci. Biotechnol. 6, 41.
    Pubmed KoreaMed CrossRef
  10. Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, Harmsen HJM, Faber KN, and Hermoso MA. 2019. Short Chain Fatty Acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front. Immunol. 10, 277.
    Pubmed KoreaMed CrossRef
  11. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, and Tyson GW. 2015. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043-1055.
    Pubmed KoreaMed CrossRef
  12. Schwiertz A, Hold GL, Duncan SH, Gruhl B, Collins MD, Lawson PA, Flint HJ, and Blaut M. 2002. Anaerostipes caccae gen. nov., sp. nov., a new saccharolytic, acetate-utilising, butyrate-producing bacterium from human faeces. Syst. Appl. Microbiol. 25, 46-51.
    Pubmed CrossRef
  13. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, and Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res. 44, 6614-6624.
    Pubmed KoreaMed CrossRef
  14. Wilson KH, Blitchington RB, and Greene RC. 1990. Amplification of bacterial 16S ribosomal DNA with polymerase chain reaction. J. Clin. Microbiol. 28, 1942-1946.
    Pubmed KoreaMed CrossRef
  15. Zhou H, Yu B, Sun J, Liu Z, Chen H, Ge L, and Chen D. 2021. Short-chain fatty acids can improve lipid and glucose metabolism independently of the pig gut microbiota. J. Anim. Sci. Biotechnol. 12, 61.
    Pubmed KoreaMed CrossRef


March 2024, 60 (1)
Full Text(PDF) Free

Social Network Service
Services

Author ORCID Information