Open Access

Non-contiguous finished genome sequence of Aminomonas paucivorans type strain (GLU-3)

  • Sam Pitluck
  • , Montri Yasawong
  • , Brittany Held,
  • , Alla Lapidus
  • , Matt Nolan
  • , Alex Copeland
  • , Susan Lucas
  • , Tijana Glavina Del Rio
  • , Hope Tice
  • , Jan-Fang Cheng
  • , Olga Chertkov,
  • , Lynne Goodwin,
  • , Roxane Tapia,
  • , Cliff Han,
  • , Konstantinos Liolios
  • , Natalia Ivanova
  • , Konstantinos Mavromatis
  • , Galina Ovchinnikova
  • , Amrita Pati
  • , Amy Chen
  • , Krishna Palaniappan
  • , Miriam Land,
  • , Loren Hauser,
  • , Yun-Juan Chang,
  • , Cynthia D. Jeffries,
  • , Rüdiger Pukall
  • , Stefan Spring
  • , Manfred Rohde
  • , Johannes Sikorski
  • , Markus Göker
  • , Tanja Woyke
  • , James Bristow
  • , Jonathan A. Eisen,
  • , Victor Markowitz
  • , Philip Hugenholtz
  • , Nikos C. Kyrpides
  • and Hans-Peter Klenk
Corresponding author

DOI: 10.4056/sigs.1253298

Received: 20 November 2010

Published: 31 December 2010


Aminomonas paucivorans Baena et al. 1999 is the type species of the genus Aminomonas, which belongs to the family Synergistaceae. The species is of interest because it is an asaccharolytic chemoorganotrophic bacterium which ferments quite a number of amino acids. This is the first finished genome sequence (with one gap in a rDNA region) of a member of the genus Aminomonas and the third sequence from the family Synergistaceae. The 2,630,120 bp long genome with its 2,433 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.


strictly anaerobicobligate amino-acid-degradingGram-negativenonmotileasaccharolyticmesophilicchemoorganotrophicSynergistaceae‘SynergistetesGEBA


Strain GLU-3T (= DSM 12260 = ATCC BAA-6) is the type strain of the species Aminomonas paucivorans, which in turn is the type and only species of the genus Aminomonas [1,2]. The generic name derives from the Latin word ‘aminum’ meaning ‘amine’ and the Greek word ‘monas’ meaning ‘a unit or monad’, referring to amine-degrading monads [2]. The species epithet is derived from the Latin word ‘paucus’ meaning ‘few or little’ and the Latin word ‘vorans’ meaning ‘digesting’, referring to digesting little [2]. Strain GLU-3T was isolated from anaerobic sludge of a dairy wastewater treatment plant in SantaFe de Bogota, Colombia [2]. So far, no further isolates have been obtained for A. paucivorans. Here we present a summary classification and a set of features for A. paucivorans GLU-3T, together with the description of the non-contiguous finished genomic sequencing and annotation.

Classification and features

The 16S rRNA gene of A. paucivorans GLU-3T shares 96% sequence identity with that of the type strain of Thermanaerovibrio acidaminovorans, which was isolated from an upflow anaerobic sludge bed reactor of a sugar refinery, Breda, the Netherlands [3] (Figure 1), and 82.2-96.4% sequence identity with the type strains from the other members of the family Synergistaceae [11]. The sequences of four marine metagenomic clones in the env_nt database, 1096626071844 (AACY020063505), 1096626840052 (AACY020539193), 1096626748225 (AACY020105546) and 1096626774924 (AACY020274567) share 96% sequence identity with A. paucivorans GLU-3T (as of October 2010). A representative genomic 16S rRNA sequence of A. paucivorans was compared using NCBI BLAST under default values with the most recent release of the Greengenes database [12] and the relative frequencies of taxa and keywords, weighted by BLAST scores, were determined. The four most frequent genera were Thermanaerovibrio (65.5%), Aminomonas (18.0%), Anaerobaculum (9.0%) and Aminiphilus (7.6%). The species yielding the highest score was T. acidaminovorans. The five most frequent keywords within the labels of environmental samples which yielded hits were 'anaerobic' (7.2%), 'sludge' (6.9%), 'wastewater' (6.8%), 'municipal' (6.8%) and 'digester' (6.7%). These keywords corroborate the physiological and ecological features on strain GLU-3T as depicted in the original description [2].The single most frequent keyword within the labels of environmental samples which yielded hits of a higher score than the highest scoring species was 'harbor/sediment' (50.0%).

Figure 1

Phylogenetic tree highlighting the position of A. paucivorans GLU-3T relative to the other type strains within the family Synergistaceae. The tree was inferred from 1,347 aligned characters [4,5] of the 16S rRNA gene sequence under the maximum likelihood criterion [6] and rooted in accordance with the current taxonomy. The branches are scaled in terms of the expected number of substitutions per site. Numbers above branches are support values from 1,000 bootstrap replicates [7] if larger than 60%. Lineages with type strain genome sequencing projects registered in GOLD [8] are shown in blue, published genomes in bold [3,9,10].

Figure 1 shows the phylogenetic neighborhood of A. paucivorans GLU-3T in a 16S rRNA based tree. The sequences of the three 16S rRNA gene copies in the genome of A. paucivorans differ from each other by up to one nucleotide, and differ by up to eleven nucleotides from the previously published 16S rRNA sequence (AF072581), which contains 59 ambiguous base calls (ambiguous bases not count as differences).

A. paucivorans GLU-3T is described as Gram-negative, slightly curved, rod-shaped bacterium (0.3 × 4.0-6.0 µm), which occurs singly or in pairs (Figure 2 and Table 1). Colonies of strain GLU-3T are round, smooth and white, with a diameter up to 1 mm [2]. Strain GLU-3T does not produce endospores [2]. The organism does not have flagella and motility is not observed [2], although plenty of motility genes are present in the genome. Strain GLU-3T is a strictly anaerobic, mesophilic, chemoorganotrophic and asaccharolytic bacterium [2]. The temperature range for growth is 20-40°C, with an optimum at 35°C [2]. The pH range for growth is 6.7-8.3, with an optimum at 7.5 [2]. The organism does not require NaCl for growth but tolerates up to 2.0% [2]. The optimum growth occurs in media with 0.05-0.5% of NaCl [2]. The species requires yeast extract for growth [2]. The organism is able to ferment arginine, histidine, glutamine, threonine, and glycine [2]. Arginine is fermented to acetate, formate and ornithine [2]. Histidine is fermented to acetate and formate [2]. Glutamate is fermented to acetate, formate and trace amounts of propionate [2]. Threonine and glycine are fermented to acetate [2]. Casamino acid, peptone and cysteine are only poorly used by the strain GLU-3T, and acetate is the end-product of the amino acid metabolism [2]. A mixed culture of strain GLU-3T and Methanobacterium formicicum does not extend the range of substrate utilization [2], as is observed for, e.g., Aminobacterium colombiense - [9]. Methane is not detectable in mixed cultures, when grown in glycine and threonine [2], however, the end-product profiles are the same as in pure culture [2]. The major end-product is shifted from acetate to propionate, when strain GLU-3T was grown together with M. formicicum on arginine, histidine and glutamate [2]. Ornithine is not accumulated during arginine degradation in mixed culture [2]. Strain GLU-3T does not degrade alanine and branched-chain amino acids, valine, leucine and isoleucine either in pure culture or in syntrophic growth with M. formicicum [2]. Also, the range of amino acid utilization is not increased in co-culture with M. formicicum [2]. Strain GLU-3T does not grow on carbohydrates, gelatin, casein, pyruvate, succinate, malate, fumarate, α-ketoglutarate, mesaconate, β-methylaspartate, oxaloacetate, glycerol, ethanol, acetate, propionate, butyrate, lactate, citrate, leucine, lysine, alanine, valine, proline, serine, methionine, asparagines, phenylalanine and aspartate [2]. The organism does not utilize sulfate, thiosulfate, elemental sulfur, sulfite, nitrate and fumarate as electron acceptors [2].

Figure 2

Scanning electron micrograph of A. paucivorans GLU-3T

Table 1

Classification and general features of A. paucivorans GLU-3T according to the MIGS recommendations [13].




   Evidence code

   Current classification

   Domain Bacteria

   TAS [14]

   Phylum “Synergistetes

   TAS [15]

   Class Synergistia

   TAS [15]

   Order Synergistales

   TAS [15]

   Family Synergistaceae

   TAS [15]

   Genus Aminomonas

   TAS [2]

   Species Aminomonas paucivorans

   TAS [2]

   Type strain GLU-3

   TAS [2]

   Gram stain


   TAS [2]

   Cell shape

   slightly curved rods occurring singly   or in pairs

   TAS [2]



   TAS [2]



   TAS [2]

   Temperature range


   TAS [2]

   Optimum temperature


   TAS [2]


   0-2% NaCl (optimum 0.05-0.50%)

   TAS [2]


   Oxygen requirement

   strictly anaerobic

   TAS [2]

   Carbon source

   amino acids

   TAS [2]

   Energy source


   TAS [2]




   TAS [2]


   Biotic relationship







   Biosafety level


   TAS [16]


   anaerobic sludge of a dairy   wastewater treatment plant

   TAS [2]


   Geographic location

   SantaFe de Bogota, Colombia

   TAS [2]


   Sample collection time













   not reported



   2620 m


Evidence codes - IDA: Inferred from Direct Assay (first time in publication); TAS: Traceable Author Statement (i.e., a direct report exists in the literature); NAS: Non-traceable Author Statement (i.e., not directly observed for the living, isolated sample, but based on a generally accepted property for the species, or anecdotal evidence). These evidence codes are from of the Gene Ontology project [17]. If the evidence code is IDA, then the property was directly observed by one of the authors or an expert mentioned in the acknowledgements.


No chemotaxonomic data are currently available for A. paucivorans or for other members of the genus Aminomonas.

Genome sequencing and annotation

Genome project history

This organism was selected for sequencing on the basis of its phylogenetic position [18], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [19]. The genome project is deposited in the Genome OnLine Database [8,20] and the non-contiguous finished genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession AEIV00000000. The version described in this paper is the first version, AEIV01000000. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2.

Table 2

Genome sequencing project information





    Finishing quality

    Non-contiguous finished


    Libraries used

    Three genomic libraries: one 454 pyrosequence standard library,    454 PE library (12 kb insert size),    one Illumina standard library


    Sequencing platforms

    454 GS FLX Titanium, Illumina GAii


    Sequencing coverage

    202.0 × Illumina; 72.4× pyrosequence



    Newbler version    PostRelease-11-05-2008-gcc-3.4.6,    phrap


    Gene calling method

    Prodigal 1.4, GenePRIMP


    CM001022, AEIV00000000

    Genbank Date of Release

    November 2, 2010



    NCBI project ID


    Database: IMG-GEBA



    Source material identifier

    DSM 12260

    Project relevance

    Tree of Life, GEBA

Growth conditions and DNA isolation

A. paucivorans GLU-3T, DSM 12260, was grown anaerobically in DSMZ medium 846 (Anaerobic Serine/Arginine medium) [21] at 37°C. DNA was isolated from 0.5-1 g of cell paste using the MasterPure Gram-positive DNA purification kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer, with modification st/LALM for cell lysis as described in Wu et al. [19].

Genome sequencing and assembly

The genome was sequenced using a combination of Illumina and 454 sequencing platforms. All general aspects of library construction and sequencing can be found at the JGI website [22]. Pyrosequencing reads were assembled using the Newbler assembler version (Roche). The initial Newbler assembly consisted of 126 contigs in 103 scaffolds and was converted into a phrap assembly by making fake reads from the consensus for collecting the read pairs in the 454 paired end library. Illumina GAii sequencing data (525.3 Mb) was assembled with Velvet [23] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 190.7 Mb 454 draft data and all of the 454 paired end data. Newbler parameters were -consed -a 50 -l 350 -g -m -ml 20.

The Phred/Phrap/Consed software package [24] was used for sequence assembly and quality assessment in the subsequent finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution (Web Site), Dupfinisher, or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI) [25]. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks (J.-F.Chang, unpublished). A total of 259 additional reactions were necessary to close gaps and to raise the quality of the finished sequence. Illumina reads were also used to correct potential base errors and increase consensus quality using a software (Polisher) developed at JGI [26]. The error rate of the completed genome sequence is less than 1 in 100,000. Together, the combination of the Illumina and 454 sequencing platforms provided 274.4× coverage of the genome. The final assembly contained 535, 052 pyrosequences and 15,007,632 Illumina reads.

Genome annotation

Genes were identified using Prodigal [27] as part of the Oak Ridge National Laboratory genome annotation pipeline, followed by a round of manual curation using the JGI GenePRIMP pipeline [28]. The predicted CDSs were translated and used to search the National Center for Biotechnology Information (NCBI) nonredundant database, UniProt, TIGR-Fam, Pfam, PRIAM, KEGG, COG, and InterPro databases. Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes - Expert Review (IMG-ER) platform [29].

Genome properties

The genome consists of a 2,630,120 bp long chromosome with an overall GC content of 67.6% (Table 3 and Figure 3). Of the 2,494 genes predicted, 2,433 were protein-coding genes, and 61 RNAs; 34 pseudogenes were also identified. The majority of the protein-coding genes (77.2%) were assigned with a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3

Genome Statistics



   % of Total

Genome size (bp)



DNA Coding region (bp)



DNA G+C content (bp)



Number of replicons


Extrachromosomal elements


Total genes



RNA genes



rRNA operons


Protein-coding genes



Pseudo genes



Genes with function prediction



Genes in paralog clusters



Genes assigned to COGs



Genes assigned Pfam domains



Genes with signal peptides



Genes with transmembrane helices



CRISPR repeats


Figure 3

Graphical circular map of the genome. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Table 4

Number of genes associated with the general COG functional categories








Translation, ribosomal structure and biogenesis




RNA processing and modification








Replication, recombination and repair




Chromatin structure and dynamics




Cell cycle control, cell division, chromosome partitioning




Nuclear structure




Defense mechanisms




Signal transduction mechanisms




Cell wall/membrane/envelope biogenesis




Cell motility








Extracellular structures




Intracellular trafficking, secretion, and vesicular transport




Posttranslational modification, protein turnover, chaperones




Energy production and conversion




Carbohydrate transport and metabolism




Amino acid transport and metabolism




Nucleotide transport and metabolism




Coenzyme transport and metabolism




Lipid transport and metabolism




Inorganic ion transport and metabolism




Secondary metabolites biosynthesis, transport and catabolism




General function prediction only




Function unknown




Not in COGs



We would like to gratefully acknowledge the help of Katja Steenblock for growing A. paucivorans cultures and Susanne Schneider for DNA extraction and quality analysis (both at DSMZ). This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396, UT-Battelle and Oak Ridge National Laboratory under contract DE-AC05-00OR22725, as well as German Research Foundation (DFG) INST 599/1-2 and Thailand Research Fund Royal Golden Jubilee Ph.D. Program No. PHD/0019/2548 for MY.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


  1. Garrity G. NamesforLife. BrowserTool takes expertise out of the database and puts it right in the browser. Microbiol Today. 2010; 37:9
  2. Baena S, Fardeau ML, Ollivier B, Labat M, Thomas P, Garcia JL and Patel BK. Aminomonas paucivorans gen. nov., sp. nov., a mesophilic, anaerobic, amino-acid-utilizing bacterium. Int J Syst Bacteriol. 1999; 49:975-982 View ArticlePubMed
  3. Chovatia M, Sikorski J, Schröder M, Lapidus A, Nolan M, Tice H, Glavina Del Rio T, Copeland A, Cheng JF and Lucas S. Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T). Stand Genomic Sci. 2009; 1:254-261 View Article
  4. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 2000; 17:540-552PubMed
  5. Lee C, Grasso C and Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformatics. 2002; 18:452-464 View ArticlePubMed
  6. Stamatakis A, Hoover P and Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 2008; 57:758-771 View ArticlePubMed
  7. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME and Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci. 2009; 5541:184-200 View Article
  8. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM and Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2009; 38:D346-D354 View ArticlePubMed
  9. Chertkov O, Sikorski J, Brambilla E, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Lucas S, Tice H and Cheng JF. Complete genome sequence of Aminobacterium colombiense type strain (ALA-1T). Stand Genomic Sci. 2010; 2:280-289 View Article
  10. LaButti K, Mayilraj S, Clum A, Lucas S, Glavina Del Rio T, Nolan M, Tice H, Cheng JF, Pitluck S and Liolios K. Permanent draft genome sequence of Dethiosulfovibrio peptidovorans type strain (SEBR 4207T). Stand Genomic Sci. 2010; 3:85-92 View Article
  11. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK and Lim YW. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol. 2007; 57:2259-2261 View ArticlePubMed
  12. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, Huber T, Dalevi D, Hu P and Andersen GL. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006; 72:5069-5072 View ArticlePubMed
  13. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ and Angiuoli SV. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol. 2008; 26:541-547 View ArticlePubMed
  14. Woese CR, Kandler O and Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA. 1990; 87:4576-4579 View ArticlePubMed
  15. Jumas-Bilak E, Roudiere L and Marchandin H. Description of 'Synergistetes' phyl. nov. and emended description of the phylum 'Deferribacteres' and of the family Syntrophomonadaceae, phylum 'Firmicutes'. Int J Syst Evol Microbiol. 2009; 59:1028-1035 View ArticlePubMed
  16. . Classification of bacteria and archaea in risk groups. [Bundesanstalt für Arbeitsschutz und Arbeitsmedizin, Germany.]. TRBA. 2005; 466:18
  17. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS and Eppig JT. Gene Ontology: tool for the unification of biology. Nat Genet. 2000; 25:25-29 View ArticlePubMed
  18. Klenk HP and Goeker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol. 2010; 33:175-182 View ArticlePubMed
  19. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M and Tindall BJ. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature. 2009; 462:1056-1060 View ArticlePubMed
  20. Liolios K, Mavromatis K, Tavernarakis N and Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008; 36:D475-D479 View ArticlePubMed
  21. List of growth media used at DSMZ: Web Site
  22. . Web Site
  23. Zerbino DR and Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008; 18:821-829 View ArticlePubMed
  24. Phrap and Phred for Windows. MacOS, Linux, and Unix. http://Web Site
  25. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F and Lucas S. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci. 2009; 1:12-20 View Article
  26. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for using ultra short reads in microbial genome assembly and finishing. AGBT, Marco Island, FL, 2008.
  27. Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW and Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010; 11:119 View ArticlePubMed
  28. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A and Kyrpides NC. GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods. 2010; 7:455-457 View ArticlePubMed
  29. Markowitz VM, Ivanova NN, Chen IMA, Chu K and Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics. 2009; 25:2271-2278 View ArticlePubMed