Genome sequence data and properties of Bifidobacterium bifidum strain ICIS-504 isolated from multispecies bifidobacterial community

This report presents the data on the draft genome sequence of Bifidobacterium bifidum strain ICIS-504. The strain, isolated from the intestine of a 41-year-old healthy woman is a member of community consist of four strains of three bifidobacterial species: B. longum, B. bifidum and B. breve. Annotation of the genome sequence revealed as high similarity with deposited strains as the unique duplication in the functional region of the only AmiR-family response regulator gene. The draft genome sequence data of B. bifidum strain ICIS-504 is available under the accession nos. JAJJPE000000000.1, PRJNA776132 and SAMN22746550 for NCBI Genome, Bioproject and Biosample databases, respectively.


Specifications
'Microbiology' Specific subject area Microbial genomics of beneficial bacteria Type of data Genome assembly, predicted genes and annotation How data were acquired Whole genome sequencing of fragment libraries with Illumina MiSeq platform, following de novo genomic assembly Data format FASTA format for genome sequences GenBank format for genome annotations Parameters for data collection The genomic DNA extraction, fragment library preparation, Illumina sequencing, de novo assembly and annotation procedures Description of data collection The genomic DNA extraction was performed using the standard phenol-chloroform method; fragment library was prepared by using Illumina, San Diego, CA Kit. The library was sequenced in a 2 × 300-nucleotide run using the MiSeq reagent kit version 3 and MiSeq desktop sequencer (Illumina).
The reads were quality trimmed using the sliding window mode of the

Value of the Data
• Presented strain is a member of multispecies community of human intestinal residential bifidobacteria. • The described immunoregulatory properties of the presented strain will make it possible to clarify the adaptive potential of B. bifidum bacteria in the multispecies consortium of indigenous bacteria of the human intestine. • High similarity with deposited genomes of B. bifidum strains combined with the unique duplication in the functional region of the only AmiR-family response regulator gene makes the presented strain a valuable object for further functional studies.

Data
The case of four strains of bifidobacteria isolated at once was of particular interest to us. We determined a number of phenotypic properties in the isolated strains and sequenced two strains: B. longum ICIS-505 [1] and B. bifidum ICIS-504, the results of which we present in this communication with an emphasis on the most variable determinants important for bifidobacteria adaptability in the biotope: the set of sortase-dependent fimbriae [2] and two-component signaling systems [3] .
Sequencing of the strain genome and annotation of the sequences obtained showed unambiguous belonging of the strain to the B. bifidum species and high similarity of its genome sequence with the previously sequenced strain B. bifidum MRI 1 (Institute of Fundamental Science, Pohang University of Science and Technology, Korea, NCBI Reference Sequence Index: NZ_CP018757.1). The strains are characterized by an average number of sortase-dependent fimbriae determinants (4 genes with an LPxTG domain) and a small number of genes of twocomponent signaling systems: 5 serine-threonine protein kinases, 8 histidine kinases, and 13 response regulators.
Analysis of the amino acid sequence WP_229940945.1 of the AmiR family response regulator showed that the heptadic repeat duplication LKKAEEK, unique among the deposited genomes, is located in the central region of the helix, which provides the formation of a functional dimer [4] . At the same time, it has been shown that the length of this region is a conserved trait and is probably reflected in the function of the resulting polypeptide [5] .

Materials and Methods
The studied strains were cultured in 4 ml of Schadler's broth (HiMedia Laboratories Pvt. Limited) for 48 h in an atmosphere of 0.6% oxygen and 5% carbon dioxide at 37 C, as described in [6] . DNA isolation, library preparation, sequencing, as well as genome assembly and annotation were performed in full accordance with the technique described in our previous work. Bifidobacteria production of SCFAs was determined by gas chromatography: cultured samples were centrifuged at 13600 g for 15 min, and 50 μl of 98% sulfuric acid (Panreac, Germany) was added to 500 μl of the supernatant. Extraction of volatile fatty acids from the samples was performed in 750 μl isobutyl alcohol (Sigma-Aldrich, USA) and the process was repeated twice. Acetate extraction was performed in a GC-2010 Plus gas-liquid chromatograph (Shimadzu, Japan) equipped with a flame ionization detector with a HP-FFAP capillary column (Agilent Technologies, USA), diameter 0.32 mm, length 50 meters. Evaporator temperature was 240 °C; temperature program for capillary column: 0 min -70 °C, 10 min -160 °C, 5 min -180 °C and 25 min -240 °C; detector temperature -260 °C. Helium was used as a carrier gas, the carrier gas speed was 21 cm/s. The peak area concentrations were calculated using GCsolution software (Shimadzu, Japan). To assess the immunoregulatory activity of bifidobacteria, we determined the ability of mononuclear cells isolated and incubated according to the method of previous work [6] to produce the indicated cytokines in concentrations measured by enzyme immunoassay using the method described in [7] .

Ethics Statements
This work did not contain human subjects, animals, cell lines or endangered species.

Declaration of Competing Interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.