AI Chat Paper
Note: Please note that the following content is generated by AMiner AI. SciOpen does not take any responsibility related to this content.
{{lang === 'zh_CN' ? '文章概述' : 'Summary'}}
{{lang === 'en_US' ? '中' : 'Eng'}}
Chat more with AI
Home Food Science Article
PDF (7.7 MB)
Collect
Submit Manuscript AI Chat Paper
Show Outline
Outline
Show full outline
Hide outline
Outline
Show full outline
Hide outline
Publishing Language: Chinese | Open Access

Comparative Genomic Analysis of Bifidobacterium Based on Glycoside Hydrolase Family Genes and Its Application in the Isolation of B. bifidum

Yan LI Hang YUSiyuan CHENNan JIANGPenghao ZHAOXiangchen MENG ( )
Key Laboratory of Dairy Science, Ministry of Education, Northeast Agricultural University, Harbin 150030, China
Show Author Information

Abstract

This study aimed to comparatively analyze the common and unique glycoside hydrolase (GH) family genes in Bifidobacterium. On this basis, a rapid method for isolating target Bifidobacterium strains from infant fecal samples was developed. The GH family genes of four bifidobacterial taxa, including B. breve, B. longum subsp. longum, B. bifidum and B. longum subsp. infantis, were compared, revealing that there were common and unique patterns in the GH family genes among these species, which could serve as molecular markers for the isolation and identification of Bifidobacterium strains. Based on colony polymerase chain reaction (PCR) and nucleic acid electrophoresis, a rapid method for the isolation and identification of the aforementioned bifidobacterial strains were successfully developed and applied to the isolation of B. bifidum. This method is characterized by not only high efficiency of isolation but also low costs. The results of this study contribute to a better understanding of the diversity of Bifidobacterium, thereby laying a foundation for future probiotic research and development.

CLC number: Q93 Document code: A Article ID: 1002-6630(2025)05-0114-10

References

[1]

VENTURA M, VAN SINDEREN D, FITZGERALD G F, et al. Insights into the taxonomy, genetics and physiology of bifidobacteria[J]. Antonie van Leeuwenhoek, 2004, 86(3): 205-223. DOI:10.1023/B:ANTO.0000047930.11029.ec.

[2]

LUGLI G A, MILANI C, TURRONI F, et al. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family[J]. BMC Genomics, 2017, 18(1): 568. DOI:10.1186/s12864-017-3955-4.

[3]

LEE S Y, LEE B H, PARK J H, et al. Bifidobacterium bifidum BGN4 paraprobiotic supplementation alleviates experimental colitis by maintaining gut barrier and suppressing nuclear factor kappa B activation signaling molecules[J]. Journal of Medicinal Food, 2022, 25(2): 146-157. DOI:10.1089/jmf.2021.K.0150.

[4]

TANG N, YU Q Q, MEI C X, et al. Bifidobacterium bifidum CCFM1163 alleviated cathartic colon by regulating the intestinal barrier and restoring enteric nerves[J]. Nutrients, 2023, 15(5): 1146. DOI:10.3390/nu15051146.

[5]

MILANI C, TURRONI F, DURANTI S, et al. Genomics of the genus Bifidobacterium reveals species-specific adaptation to the glycan-rich gut environment[J]. Applied and Environmental Microbiology, 2015, 82(4): 980-991. DOI:10.1128/AEM.03500-15.

[6]

TURNBAUGH P J, RIDAURA V K, FAITH J J, et al. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice[J]. Science Translational Medicine, 2009, 1(6): 6ra14. DOI:10.1126/scitranslmed.3000322.

[7]

KOENIG J E, SPOR A, SCALFONE N, et al. Succession of microbial consortia in the developing infant gut microbiome[J]. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108(Suppl 1): 4578-4585. DOI:10.1073/pnas.1000081107.

[8]

REENS A L, COSETTA C M, SAUR R, et al. Tunable control of B. infantis abundance and gut metabolites by co-administration of human milk oligosaccharides[J]. Gut Microbes, 2024, 16(1): 2304160. DOI:10.1080/19490976.2024.2304160.

[9]

KATOH T, YAMADA C, WALLACE M D, et al. A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem[J]. Nature Chemical Biology, 2023, 19(6): 778-789. DOI:10.1038/s41589-023-01272-y.

[10]

ABDELHAMID A, EL-DOUGDOUG N K. Comparative genomics of the gut commensal Bifidobacterium bifidum reveals adaptation to carbohydrate utilization[J]. Biochemical and Biophysical Research Communications, 2021, 547: 155-161. DOI:10.1016/j.bbrc.2021.02.046.

[11]

YAMADA C, GOTOH A, SAKANAKA M, et al. Molecular insight into evolution of symbiosis between breast-fed infants and a member of the human gut microbiome Bifidobacterium longum[J]. Cell Chemical Biology, 2017, 24(4): 515-524. DOI:10.1016/j.chembiol.2017.03.012.

[12]

LI X X, YANG J J, SHI S Q, et al. The genome of Bifidobacterium longum subsp. infantis YLGB-1496 provides insights into its carbohydrate utilization and genetic stability[J]. Genes, 2024, 15(4): 466. DOI:10.3390/genes15040466.

[13]

WEI X J, YU L L, ZHANG C, et al. Genetic-phenotype analysis of Bifidobacterium bifidum and its glycoside hydrolase gene distribution at different age groups[J]. Foods, 2023, 12(5): 922. DOI:10.3390/foods12050922.

[14]

WINAND R, BOGAERTS B, HOFFMAN S, et al. Targeting the 16S rRNA gene for bacterial identification in complex mixed samples: comparative evaluation of second (Illumina) and third (Oxford Nanopore Technologies) generation sequencing technologies[J]. International Journal of Molecular Sciences, 2019, 21(1): 298. DOI:10.3390/ijms21010298.

[15]

JOHNSON J S, SPAKOWICZ D J, HONG B Y, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis[J]. Nature Communications, 2019, 10(1): 5029. DOI:10.1038/s41467-019-13036-1.

[16]

JAIN C, RODRIGUEZ-R L M, PHILLIPPY A M, et al. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries[J]. Nature Communications, 2018, 9(1): 5114. DOI:10.1038/s41467-018-07641-9.

[17]

MARCHIN M, KELLY P T, FANG J W. Tracker: continuous HMMER and BLAST searching[J]. Bioinformatics, 2005, 21(3): 388-389. DOI:10.1093/bioinformatics/bti012.

[18]

YANG H, XIONG J, HE L P, et al. Stress tolerance, safety, and probiotic traits of cholesterol-decreasing Bifidobacterium BLH1 isolated from Guizhou red sour soup, a traditional Chinese fermented food[J]. LWT-Food Science and Technology, 2024, 192: 115696. DOI:10.1016/j.lwt.2023.115696.

[20]

LYU F Y, HAN F R, GE C L, et al. OmicStudio: a composable bioinformatics cloud platform with real-time feedback that can generate high-quality graphs for publication[J]. iMeta, 2023, 2(1): e85. DOI:10.1002/imt2.85.

[21]

CASTILLO-RAMÍREZ S. On the road to genomically defining bacterial intra-species units[J]. mSystems, 2024, 9(7): e0058424. DOI:10.1128/msystems.00584-24.

[22]

MATSUMOTO T, SHIMADA S, HATA Y, et al. Multi-functional glycoside hydrolase: blon_0625 from Bifidobacterium longum subsp. infantis ATCC 15697[J]. Enzyme and Microbial Technology, 2015, 68: 10-14. DOI:10.1016/j.enzmictec.2014.10.001.

[23]

WEE S K, CHAN M B P, SIVALINGAM S P, et al. Pre-isolation molecular screening for high-throughput sampling and sequencing of bacterial microbes from the environment[J]. Current Protocols, 2023, 3(5): e778. DOI:10.1002/cpz1.778.

[24]

LIU K X, WANG Y J, ZHAO M L, et al. Rapid discrimination of Bifidobacterium longum subspecies based on MALDI-TOF MS and machine learning[J]. Frontiers in Microbiology, 2023, 14: 1297451. DOI:10.3389/fmicb.2023.1297451.

[25]

YOON S H, HA S M, LIM J, et al. A large-scale evaluation of algorithms to calculate average nucleotide identity[J]. Antonie Van Leeuwenhoek, 2017, 110(10): 1281-1286. DOI:10.1007/s10482-017-0844-4.

[26]

HERNÁNDEZ-RODRÍGUEZ D, VÁSQUEZ-AGUILAR A A, SERIO-SILVA J C, et al. Molecular detection of Bifidobacterium spp. in faeces of black howler monkeys (Alouatta pigra)[J]. Journal of Medical Primatology, 2019, 48(2): 99-105. DOI:10.1111/jmp.12395.

[27]

BOLZON V, PESANDO M, BULFONI M, et al. An integrated analytical approach for the characterization of probiotic strains in food supplements[J]. Nutrients, 2022, 14(23): 5085. DOI:10.3390/nu14235085.

[28]

BLANCO G, RUIZ L, TAMÉS H, et al. Revisiting the metabolic capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a glycoside hydrolase perspective[J]. Microorganisms, 2020, 8(5): 723. DOI:10.3390/microorganisms8050723.

[29]

XIAO M F, ZHANG C, DUAN H, et al. Cross-feeding of bifidobacteria promotes intestinal homeostasis: a lifelong perspective on the host health[J]. NPJ Biofilms and Microbiomes, 2024, 10(1): 47. DOI:10.1038/s41522-024-00524-6.

Food Science
Pages 114-123
Cite this article:
LI Y, YU H, CHEN S, et al. Comparative Genomic Analysis of Bifidobacterium Based on Glycoside Hydrolase Family Genes and Its Application in the Isolation of B. bifidum. Food Science, 2025, 46(5): 114-123. https://doi.org/10.7506/spkx1002-6630-20240913-113

87

Views

5

Downloads

0

Crossref

0

Scopus

0

CSCD

Altmetrics

Received: 13 September 2024
Published: 15 March 2025
© Beijing Academy of Food Sciences 2025.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Return