Next Article in Journal
SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples
Next Article in Special Issue
Altered in Vitro Metabolomic Response of the Human Microbiota to Sweeteners
Previous Article in Journal
Three New Mutations and Mild, Asymmetrical Phenotype in the Highly Distinctive LAMM Syndrome: A Report of Eight Further Cases
Previous Article in Special Issue
Obesity, Xenobiotic Intake and Antimicrobial-Resistance Genes in the Human Gastrointestinal Tract: A Comparative Study of Eutrophic, Overweight and Obese Individuals
Open AccessArticle

groEL Gene-Based Phylogenetic Analysis of Lactobacillus Species by High-Throughput Sequencing

1,2, 1,2, 1,2, 1,2, 1,2,3,4,*, 1,2,3, 1,2,3,4,5 and 1,2,3,6
1
State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
2
School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
3
National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
4
Yangzhou Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
5
Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
6
Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing 100048, China
*
Author to whom correspondence should be addressed.
Genes 2019, 10(7), 530; https://doi.org/10.3390/genes10070530
Received: 18 April 2019 / Revised: 27 June 2019 / Accepted: 8 July 2019 / Published: 12 July 2019
(This article belongs to the Special Issue Human Microbiome or Microbial Communities Related with Humans)
  |  
PDF [1487 KB, uploaded 15 July 2019]
  |  

Abstract

Lactobacillus is a fairly diverse genus of bacteria with more than 260 species and subspecies. Many profiling methods have been developed to carry out phylogenetic analysis of this complex and diverse genus, but limitations remain since there is still a lack of comprehensive and accurate analytical method to profile this genus at species level. To overcome these limitations, a Lactobacillus-specific primer set was developed targeting a hypervariable region in the groEL gene—a single-copy gene that has undergone rapid mutation and evolution. The results showed that this methodology could accurately perform taxonomic identification of Lactobacillus down to the species level. Its detection limit was as low as 104 colony-forming units (cfu)/mL for Lactobacillus species. The assessment of detection specificity using the Lactobacillus groEL profiling method found that Lactobacillus, Pediococcus, Weissella, and Leuconostoc genus could be distinguished, but non-Lactobacillus Genus Complex could not be detected. The groEL gene sequencing and Miseq high-throughput approach were adopted to estimate the richness and diversity of Lactobacillus species in different ecosystems. The method was tested using kurut (fermented yak milk) samples and fecal samples of human, rat, and mouse. The results indicated that Lactobacillus mucosae was the predominant gut Lactobacillus species among Chinese, and L. johnsonii accounted for the majority of lactobacilli in rat and mouse gut. Meanwhile, L. delbrueckii subsp. bulgaricus had the highest relative abundance of Lactobacillus in kurut. Thus, this groEL gene profiling method is expected to promote the application of Lactobacillus for industrial production and therapeutic purpose. View Full-Text
Keywords: Lactobacillus; groEL; phylogenetic analysis; species diversity; MiSeq Illumina sequencing platform Lactobacillus; groEL; phylogenetic analysis; species diversity; MiSeq Illumina sequencing platform
Figures

Graphical abstract

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).

Supplementary material

SciFeed

Share & Cite This Article

MDPI and ACS Style

Xie, M.; Pan, M.; Jiang, Y.; Liu, X.; Lu, W.; Zhao, J.; Zhang, H.; Chen, W. groEL Gene-Based Phylogenetic Analysis of Lactobacillus Species by High-Throughput Sequencing. Genes 2019, 10, 530.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Genes EISSN 2073-4425 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top