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Announcement
18 January 2018

Draft Genome Sequences of Strains TRE 1, TRE D, TRE H, and TRI 7, Isolated from Tamarins and Belonging to Four Putative Novel Bifidobacterium Species

ABSTRACT

Bifidobacterium sp. strains TRE 1, TRE D, TRE H, and TRI 7 were isolated from two tamarins housed in Parco Natura Viva, Garda Zoological Park S.r.l. (Bussolengo, Verona, Italy). These strains belong to four putative novel species of the genus Bifidobacterium. The genome sizes were 2.7 Mb for TRE 1, 2.7 Mb for TRE D, 2.4 Mb for TRE H, and 2.7 Mb for TRI 7. The average GC contents were 63.18% for TRE 1, 58.27% for TRE D, 57.11% for TRE H, and 63.79% for TRI 7.

GENOME ANNOUNCEMENT

Bifidobacteria are Gram-positive bacteria with high G+C contents that are commonly found in the human and animal gastrointestinal tracts. Bifidobacteria are considered key commensals in host-microbe interactions, and they are believed to play a crucial role in nutrition, immunomodulation, and resistance to infection. Studies on bifidobacteria from nonhuman primates have grown in recent years. Novel species within the genus Bifidobacterium isolated from the cotton-top tamarin (Saguinus oedipus) (1) and from the emperor tamarin (Saguinus imperator) (2, 3) have recently been reported.
Here, we report the draft genome sequences of four putative novel bifidobacterial strains; three were isolated from the feces of an adult subject of the cotton-top tamarin (strains TRE 1, TRE 9, and TRE H), and one (TRI 7) was from the feces of an adult subject of the emperor tamarin. Strains were grown in MRS plus 0.05% cysteine at 37°C under anaerobic conditions using the Anaerocult system. Under in vitro culture conditions, these strains were considered oxygen tolerant and microaerophilic. Cells were lysed with SDS/lysozyme treatment, and genomic DNA was extracted with a NucleoSpin tissue kit (Macharey-Nagel, Duren, Germany) according to the manufacturer’s instructions. Illumina MiSeq V3 technology for 2 × 300-bp paired-end reads was used to sequence the whole genomes (Bio-Fab s.r.l., Rome, Italy). SPAdes version 3.11 (4) was used to assemble the whole-genome sequences. The draft genome sequences were annotated using the NCBI Prokaryotic Genome Annotation Pipeline (5) and the Rapid Annotation using Subsystems Technology (RAST) server (6).
Summary data for the genome assemblies are reported in Table 1. Average nucleotide identity (ANI) analysis results between the four studied strains were always below 82.07%; two strains displaying an ANI value ≤95% are considered to belong to two distinct species. 16S rRNA sequence comparisons with all publicly available Bifidobacterium sequences showed a level of similarity below 97% for all four strains, with the only exception being strain TRE H, which had 99% DNA sequence similarity to Bifidobacterium callitrichos DSM 23968T. However, the genetic relatedness at the genomic level of this strain calculated by ANI analysis showed a level of identity of 77.82% with its nearest phylogenetic neighbor, B. callitrichos.
TABLE 1 
TABLE 1 Summary data of the genome assembly for the four putative novel Bifidobacterium species
StrainIsolate sourceNo. of
contigs
Genome
size (bp)
GC content
(%)
No. of coding
sequences
GenBank
accession no.
TRE 1Saguinus oedipus212,698,69263.182,236PEBI00000000
TRE DSaguinus oedipus222,652,36758.272,171PGLQ00000000
TRE HSaguinus oedipus342,386,95657.111,931PEBJ00000000
TRI 7Saguinus imperator482,723,40163.792,241PEBK00000000
The similarities of the four genomes with all publicly available genomes were also calculated with Mash/MinHash genome distance estimation implemented in PATRIC version 3.5.0 (7); the distance was always above 0.11. These data thus indicate that Bifidobacterium sp. strains TRE 1, TRE D, TRE H, and TRI 7 belong to four putative novel species, the full descriptions of which are still in progress.

Accession number(s).

The assembled draft genome sequences generated in this study can be found in DDBJ/ENA/GenBank under the accession numbers reported in Table 1.

REFERENCES

1.
Michelini S, Modesto M, Filippini G, Spiezio C, Sandri C, Biavati B, Pisi A, Mattarelli P. 2016. Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.). Syst Appl Microbiol 39:229–236.
2.
Modesto M, Michelini S, Sansosti MC, De Filippo C, Cavalieri D, Qvirist L, Andlid T, Spiezio C, Sandri C, Pascarelli S, Sgorbati B, Mattarelli P. 2017. Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol. Epub ahead of print.
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Duranti S, Mangifesta M, Lugli GA, Turroni F, Anzalone R, Milani C, Mancabelli L, Ossiprandi MC, Ventura M. 2017. Bifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 67:3987–3995.
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Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M, Ostell J. 2016. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624.
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Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res 42:D206–D214.
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Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, Gillespie JJ, Gough R, Hix D, Kenyon R, Machi D, Mao C, Nordberg EK, Olson R, Overbeek R, Pusch GD, Shukla M, Schulman J, Stevens RL, Sullivan DE, Vonstein V, Warren A, Will R, Wilson MJ, Yoo HS, Zhang C, Zhang Y, Sobral BW. 2014. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res 42:D581–D591.

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cover image Genome Announcements
Genome Announcements
Volume 6Number 318 January 2018
eLocator: e01449-17
PubMed: 29348339

History

Received: 1 December 2017
Accepted: 5 December 2017
Published online: 18 January 2018

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Contributors

Authors

Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy
Paola Mattarelli
Department of Agricultural Sciences, Università di Bologna, Bologna, Italy
Monica Modesto
Department of Agricultural Sciences, Università di Bologna, Bologna, Italy
Andrea Bonetti
Department of Agricultural Sciences, Università di Bologna, Bologna, Italy
Caterina Spiezio
Parco Natura Viva, Garda Zoological Park, Bussolengo, Italy
Camillo Sandri
Parco Natura Viva, Garda Zoological Park, Bussolengo, Italy
Lorenzo Morelli
Department for Sustainable Food Processes, Università Cattolica del Sacro Cuore, Piacenza, Italy

Notes

Address correspondence to Edoardo Puglisi, [email protected].

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