Rapid Identification of Bifidobacteria in Dairy Products by Gene-targeted Species-specific PCR Technique and DGGE

Hong, Wei; Chen, Ming Ju

doi:10.5713/ajas.2007.1887

Cited by 7 publications

(4 citation statements)

References 33 publications

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“…In the present study, we observed that members of the genus Bacillus and those belonging to the phylum Bacteroidetes were mainly detected after the thermophilic phase although bacteria belonging to different phyla were also detected during the early stage of composting. The PCR-DGGE method is widely used in environmental studies (White et al, 1999;Hong and Chen, 2007). However it has been reported that the banding patterns of PCR-DGGE were biased by methods of DNA extraction and PCR protocol (Eichner et al, 1999;Rolleke et al, 1999).…”

Section: Discussionmentioning

confidence: 99%

Analysis of the Structure of the Bacterial Community in the Livestock Manure-based Composting Process

Sasaki¹,

Nonaka²,

Otawa³

et al. 2009

Asian Australas. J. Anim. Sci

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We investigated the structure of bacterial communities present in livestock manure-based composting processes and evaluated the bacterial succession during the composting processes. Compost samples were derived separately from swine manure, dairy manure and sewage sludge. The structure of the bacterial community was analyzed by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) using universal eubacterial primers. The genus Bacillus and related genera were mainly detected following the thermophilic composting phase of swine and dairy manure composts, and the members of the phylum Bacteroidetes were mainly detected in the cattle manure waste-based and sewage sludge compost. We recovered and sequenced limited number of the bands; however, the PCR-DGGE analysis showed that predominant diversities during the composting processes were markedly changed. Although PCR-DGGE analysis revealed the presence of different phyla in the early stages of composting, the members of the phylum Firmicutes and Bacteroidetes were observed to be one of the predominant phyla after the thermophilic phase.

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Section: Discussionmentioning

confidence: 99%

Analysis of the Structure of the Bacterial Community in the Livestock Manure-based Composting Process

Sasaki¹,

Nonaka²,

Otawa³

et al. 2009

Asian Australas. J. Anim. Sci

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“…After establishing that the five HMO-metabolizing gene clusters can distinguish B. infantis from the rest of the B. longum group members, we assessed the suitability of using HMO-metabolizing genes to generate primers specific to B. infantis . The development of the new primer sets was motivated by realizing that the existing primers to profile B. infantis were either too broad (e.g., 16S rRNA gene [ 33 ]) or too narrow (e.g., primers targeting sialidase gene [ 32 ]). Forty-six out of 79 HMO-metabolizing genes covered were found to be in at least 85% of B. infantis strains.…”

Section: Resultsmentioning

confidence: 99%

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes

et al. 2021

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Bifidobacterium longum subsp. infantis (B. infantis) is one of a few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis. All three organisms are classified in the same species group but only B. infantis can metabolize human milk oligosaccharides (HMOs). We compared HMO-metabolizing genes across different Bifidobacterium genomes and developed B. infantis-specific primers to determine if the genes alone or the primers can be used to quickly characterize B. infantis. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, tested for its prevalence in infant gut metagenomes, and validated the results using the B. infantis-specific primers. We observed that only 15 of 203 (7.4%) children under 2 years old from a cohort of US children harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.

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“…After establishing that the five HMO-metabolizing gene clusters can distinguish B. infantis from the rest of the B. longum group members, we assessed the suitability of using HMO-metabolizing genes to generate primers specific to B. infantis. The development of the new primer sets was motivated by realizing that the existing primers to profile B. infantis were either too broad (e.g., 16S rRNA gene [ 39]) or too narrow (e.g., primers targeting sialidase gene [32]). Forty-six out of 79 HMO-metabolizing genes covered were found to be in at least 85% of B. infantis strains.…”

Section: Resultsmentioning

confidence: 99%

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes

Tso

Bonham

Fishbein

et al. 2021

Preprint

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Bifidobacterium longum subsp. infantis (B. infantis) is one of few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis, by molecular methods. These two organisms are classified in the same species group as B. infantis but do not share the ability to metabolize human milk oligosaccharides (HMOs). Here, we compared HMO-metabolizing genes across different Bifidobacterium genomes to develop B. infantis specific primers and determine if they alone can be used to quickly characterize B. infantis with shotgun metagenomic sequencing data. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, used this characterization to test for its prevalence in infants, and validated the results using the B. infantis-specific primers. By examining stool samples from a cohort of US children and pregnant women using shotgun metagenomic sequencing, we observed that only 18 of 204 (8.8%) of children under 2 years old harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.

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Rapid Identification of Bifidobacteria in Dairy Products by Gene-targeted Species-specific PCR Technique and DGGE

Cited by 7 publications

References 33 publications

Analysis of the Structure of the Bacterial Community in the Livestock Manure-based Composting Process

Analysis of the Structure of the Bacterial Community in the Livestock Manure-based Composting Process

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes

Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes

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