Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut Microbiota
<i>Bifidobacterium longum</i> subsp. <i>longum</i> is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabili...
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MDPI AG
2021-09-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/9/9/1906 |
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| author | Romina Díaz Alexis Torres-Miranda Guillermo Orellana Daniel Garrido |
| author_facet | Romina Díaz Alexis Torres-Miranda Guillermo Orellana Daniel Garrido |
| author_sort | Romina Díaz |
| collection | DOAJ |
| description | <i>Bifidobacterium longum</i> subsp. <i>longum</i> is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional diversity. In this study, 154 genomes from public databases and four new Chilean isolates were genomically compared through an in silico approach to identify genomic divergence in genes associated with carbohydrate consumption and their possible adaptations to different human intestinal niches. The pangenome of the subspecies was open, which correlates with its remarkable ability to colonize several niches. The new genomes homogenously clustered within subspecies <i>longum</i>, as observed in phylogenetic analysis. <i>B. longum</i> SC664 was different at the sequence level but not in its functions. COG analysis revealed that carbohydrate use is variable among <i>longum</i> subspecies. Glycosyl hydrolases participating in human milk oligosaccharide use were found in certain infant and adult genomes. Predictive genomic analysis revealed that <i>B. longum</i> M12 contained an HMO cluster associated with the use of fucosylated HMOs but only endowed with a GH95, being able to grow in 2-fucosyllactose as the sole carbon source. This study identifies novel genomes with distinct adaptations to HMOs and highlights the plasticity of <i>B. longum</i> subsp. <i>longum</i> to colonize the human gut microbiota. |
| first_indexed | 2024-03-10T07:24:53Z |
| format | Article |
| id | doaj.art-2d163ad2469d45808f79a07d2c217f24 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T07:24:53Z |
| publishDate | 2021-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-2d163ad2469d45808f79a07d2c217f242023-11-22T14:18:54ZengMDPI AGMicroorganisms2076-26072021-09-0199190610.3390/microorganisms9091906Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut MicrobiotaRomina Díaz0Alexis Torres-Miranda1Guillermo Orellana2Daniel Garrido3Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Santiago 7820436, ChileDepartment of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Santiago 7820436, ChileDepartment of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Santiago 7820436, ChileDepartment of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile<i>Bifidobacterium longum</i> subsp. <i>longum</i> is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional diversity. In this study, 154 genomes from public databases and four new Chilean isolates were genomically compared through an in silico approach to identify genomic divergence in genes associated with carbohydrate consumption and their possible adaptations to different human intestinal niches. The pangenome of the subspecies was open, which correlates with its remarkable ability to colonize several niches. The new genomes homogenously clustered within subspecies <i>longum</i>, as observed in phylogenetic analysis. <i>B. longum</i> SC664 was different at the sequence level but not in its functions. COG analysis revealed that carbohydrate use is variable among <i>longum</i> subspecies. Glycosyl hydrolases participating in human milk oligosaccharide use were found in certain infant and adult genomes. Predictive genomic analysis revealed that <i>B. longum</i> M12 contained an HMO cluster associated with the use of fucosylated HMOs but only endowed with a GH95, being able to grow in 2-fucosyllactose as the sole carbon source. This study identifies novel genomes with distinct adaptations to HMOs and highlights the plasticity of <i>B. longum</i> subsp. <i>longum</i> to colonize the human gut microbiota.https://www.mdpi.com/2076-2607/9/9/1906<i>Bifidobacterium longum</i> subsp. <i>longum</i>comparative genomicshuman gut microbiota |
| spellingShingle | Romina Díaz Alexis Torres-Miranda Guillermo Orellana Daniel Garrido Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut Microbiota Microorganisms <i>Bifidobacterium longum</i> subsp. <i>longum</i> comparative genomics human gut microbiota |
| title | Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut Microbiota |
| title_full | Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut Microbiota |
| title_fullStr | Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut Microbiota |
| title_full_unstemmed | Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut Microbiota |
| title_short | Comparative Genomic Analysis of Novel <i>Bifidobacterium longum</i> subsp. <i>longum</i> Strains Reveals Functional Divergence in the Human Gut Microbiota |
| title_sort | comparative genomic analysis of novel i bifidobacterium longum i subsp i longum i strains reveals functional divergence in the human gut microbiota |
| topic | <i>Bifidobacterium longum</i> subsp. <i>longum</i> comparative genomics human gut microbiota |
| url | https://www.mdpi.com/2076-2607/9/9/1906 |
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