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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0673

PubMed

34757822, Appl Environ Microbiol. 2022 Jan 25;88(2):e0170721. doi: 10.1128/AEM.01707-21. Epub 2021 Nov 10.

Characterization method

NMR,substrate binding assay,liquid chromatography and mass spectrometry

Genomic accession number

NZ_AP012330.1

Nucelotide position range

2208139-2217803

Substrate

human milk oligosaccharide

Loci

BBPC_RS08935-BBPC_RS08970

Species

Bifidobacterium pseudocatenulatum DSM20438/28026

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

- BBPC_RS08935 WP_004221027.1 0 - 2352 (-) NZ_AP012330.1:2208139-2210491 -
- BBPC_RS08940 WP_004221030.1 2378 - 3272 (-) NZ_AP012330.1:2210517-2211411 -
- BBPC_RS08945 WP_004221033.1 3268 - 4090 (-) NZ_AP012330.1:2211407-2212229 -
- BBPC_RS08950 WP_004221035.1 4100 - 4892 (-) NZ_AP012330.1:2212239-2213031 -
- BBPC_RS08955 WP_004221037.1 4907 - 6185 (-) NZ_AP012330.1:2213046-2214324 -
- BBPC_RS08960 WP_033524398.1 6276 - 7662 (-) NZ_AP012330.1:2214415-2215801 -
- BBPC_RS08965 WP_004221042.1 7776 - 8754 (-) NZ_AP012330.1:2215915-2216893 -
- BBPC_RS08970 WP_004221044.1 8753 - 9665 (-) NZ_AP012330.1:2216892-2217804 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

- 1 - 2352 (-) CAZyme: GH95| GH95 Yes
- 2379 - 3272 (-) other Yes
- 3269 - 4090 (-) other Yes
- 4101 - 4892 (-) other Yes
- 4908 - 6185 (-) other Yes
- 6277 - 7662 (-) STP: STP|SBP_bac_1 Yes
- 7777 - 8754 (-) TC: gnl|TC-DB|D6ZW62|3.A.1.1.48 Yes
- 8754 - 9665 (-) TC: gnl|TC-DB|D6ZW63|3.A.1.1.48 Yes

PUL ID

PUL0673

PubMed

34757822, Appl Environ Microbiol. 2022 Jan 25;88(2):e0170721. doi: 10.1128/AEM.01707-21. Epub 2021 Nov 10.

Title

Fucosylated Human Milk Oligosaccharide Foraging within the Species Bifidobacterium pseudocatenulatum Is Driven by Glycosyl Hydrolase Content and Specificity.

Author

Shani G, Hoeflinger JL, Heiss BE, Masarweh CF, Larke JA, Jensen NM, Wickramasinghe S, Davis JC, Goonatilleke E, El-Hawiet A, Nguyen L, Klassen JS, Slupsky CM, Lebrilla CB, Mills DA

Abstract

Human milk enriches members of the genus Bifidobacterium in the infant gut. One species, Bifidobacterium pseudocatenulatum, is found in the gastrointestinal tracts of adults and breastfed infants. In this study, B. pseudocatenulatum strains were isolated and characterized to identify genetic adaptations to the breastfed infant gut. During growth on pooled human milk oligosaccharides (HMOs), we observed two distinct groups of B. pseudocatenulatum, isolates that readily consumed HMOs and those that did not, a difference driven by variable catabolism of fucosylated HMOs. A conserved gene cluster for fucosylated HMO utilization was identified in several sequenced B. pseudocatenulatum strains. One isolate, B. pseudocatenulatum MP80, which uniquely possessed GH95 and GH29 alpha-fucosidases, consumed the majority of fucosylated HMOs tested. Furthermore, B. pseudocatenulatum SC585, which possesses only a single GH95 alpha-fucosidase, lacked the ability to consume the complete repertoire of linkages within the fucosylated HMO pool. Analysis of the purified GH29 and GH95 fucosidase activities directly on HMOs revealed complementing enzyme specificities with the GH95 enzyme preferring 1-2 fucosyl linkages and the GH29 enzyme favoring 1-3 and 1-4 linkages. The HMO-binding specificities of the family 1 solute-binding protein component linked to the fucosylated HMO gene cluster in both SC585 and MP80 are similar, suggesting differential transport of fucosylated HMO is not a driving factor in each strain's distinct HMO consumption pattern. Taken together, these data indicate the presence or absence of specific alpha-fucosidases directs the strain-specific fucosylated HMO utilization pattern among bifidobacteria and likely influences competitive behavior for HMO foraging in situ. IMPORTANCE Often isolated from the human gut, microbes from the bacterial family Bifidobacteriaceae commonly possess genes enabling carbohydrate utilization. Isolates from breastfed infants often grow on and possess genes for the catabolism of human milk oligosaccharides (HMOs), glycans found in human breast milk. However, catabolism of structurally diverse HMOs differs between bifidobacterial strains. This study identifies key gene differences between Bifidobacterium pseudocatenulatum isolates that may impact whether a microbe successfully colonizes an infant gut. In this case, the presence of complementary alpha-fucosidases may provide an advantage to microbes seeking residence in the infant gut. Such knowledge furthers our understanding of how diet drives bacterial colonization of the infant gut.