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Overview

Proteinsi <p>Number of protein entries associated with this proteome: UniProtKB entries for regular proteomes or UniParc entries for redundant proteomes (<a href="/help/proteome%5Fredundancy">more...</a>)</p> 1,566 sequences in UniParc
Gene counti <p>This is the total number of unique genes found in the proteome set, algorithmically computed. For each gene, a single representative protein sequence is chosen from the proteome. Where possible, reviewed (Swiss-Prot) protein sequences are chosen as the representatives.</p> - Download one protein sequence per gene (FASTA)
Proteome IDi <p>The proteome identifier (UPID) is the unique identifier assigned to the set of proteins that constitute the <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a>. It consists of the characters 'UP' followed by 9 digits, is stable across releases and can therefore be used to cite a UniProt proteome.<p><a href='/help/proteome_id' target='_top'>More...</a></p>UP000002343
Taxonomy580050 - Bifidobacterium animalis subsp. lactis (strain Bl-04 / DGCC2908 / RB 4825 / SD5219)
StrainBl-04 / DGCC2908 / RB 4825 / SD5219
Last modifiedJanuary 15, 2021
Genome assembly and annotationi <p>Identifier for the genome assembly (<a href="https://www.ensembl.org/Help/Faq?id=216">more...</a>)</p> GCA_000022705.1 from ENA/EMBL full
Buscoi <p>The Benchmarking Universal Single-Copy Ortholog (BUSCO) assessment tool is used, for eukaryotic and bacterial proteomes, to provide quantitative measures of UniProt proteome data completeness in terms of expected gene content. BUSCO scores include percentages of complete (C) single-copy (S) genes, complete (C) duplicated (D) genes, fragmented (F) and missing (F) genes, as well as the total number of orthologous clusters (n) used in the BUSCO assessment.</p> C:88.5%[S:87.9%,D:0.6%],F:1.7%,M:9.8%,n:356 actinobacteria_phylum_odb10
Completenessi <p>Complete Proteome Detector (CPD) is an algorithm which employs statistical evaluation of the completeness and quality of proteomes in UniProt, by looking at the sizes of taxonomically close proteomes. Possible values are 'Standard', 'Close to Standard' and 'Outlier'.</p> Close to standard (low value)

Among the members of the large, diverse, and dynamic microbial community residing in the human gastrointestinal tract (GIT), Bifidobacterium is a dominant genus considered beneficial to humans. The GIT of healthy newborns is typically colonized by bifidobacteria, especially in breast-fed infants, during the first few days of life.

Bifidobacterium animalis subsp. lactis (strain Bl-04 / DGCC2908 / RB 4825 / SD5219) is an anaerobic Gram-positive lactic acid bacterium commonly found in the guts of healthy humans and has been identified in the infant gut biota, particularly in ileal, fecal, and mucosal samples. Some strains of B. animalis subsp. lactis are able to survive in the GIT, to adhere to human epithelial cells in vitro, to modify fecal flora, to modulate the host immune response, or to prevent microbial gastroenteritis and colitis.

B. animalis subsp. lactis is reported to utilize nondigestible oligosaccharides, which may contribute to the organism's ability to compete in the human gut. Carbohydrates resistant to enzymatic degradation and not absorbed in the upper intestinal tract are a primary source of energy for microbes residing in the large intestine. The benefits associated with probiotic strains of B. animalis subsp. lactis result in their inclusion in the human diet via formulation into a large array of dietary supplements and foods, including dairy products such as yogurt. Bifidobacterium animalis subsp. lactis is the most common bifidobacterium utilized as a probiotic in commercial dairy products in North America and Europe. However, despite this commercial and probiotic significance, strain-level differentiation of B. animalis subsp. lactis strains is hindered by the high genetic similarity of these organisms, as determined by pulsed-field gel electrophoresis and other nucleic acid-based techniques, and the lack of available genomic sequence information. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the strains Bl-04 and DSM 10140 in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis. The relatively small size of the B. animalis subsp. lactis genome compared to those of other bifidobacteria is consistent with a genome simplification process that reduces biosynthetic capabilities and favors the retention and acquisition of genes involved in the utilization of a broad repertoire of carbon and nitrogen sources. This is typical of the genomic evolution of microbes that live in nutritionally rich environments, such as the human gut, and that rely on the host and other members of the intestinal flora for energy sources and metabolic intermediates. While the number of carbohydrate hydrolases is smaller for B. animalis subsp. lactis, the variety of hydrolases present suggests the ability to utilize a wide range of complex carbohydrates, including milk galactosides and undigestible plant-derived oligosaccharides. (Adaptated from PMID:19376856).

Componentsi <p>Genomic components encoding the proteome</p>

Component nameGenome Accession(s)
Component representationUniParc sequence(s)
Chromosome1566
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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