Probiotics analysis by high-throughput sequencing revealed multiple mismatches at bacteria genus level with the declared and actual composition

Syromyatnikov, Mikhail; Nesterova, Ekaterina; Gladkikh, Maria I.; Popov, Vasily N.

doi:10.1016/j.lwt.2021.113055

Cited by 8 publications

(2 citation statements)

References 43 publications

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“…Although culture-based methods have been used widely to study complex microbial communities, they are limited to their biased detection as the vast majority of these microorganisms cannot be studied under laboratory culture conditions (Koch et al, 2013). Nevertheless, the advent of molecular biology techniques, such as real-time polymerase chain reaction PCR (Fibi et al, 2016), PCR-denaturing gradient gel electrophoresis (Pindi et al, 2019), high-throughput sequencing (Syromyatnikov et al, 2022) and metagenomics (Siles et al, 2022), has helped overcome the limitations of traditional isolation and culture techniques.…”

Section: Introductionmentioning

confidence: 99%

Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting

et al. 2023

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Sauce-flavor baijiu is one of the twelve flavor types of Chinese distilled fermented product. Microbial composition plays a key role in the stacked fermentation of Baijiu, which uses grains as raw materials and produces flavor compounds, however, the active microbial community and its relationship remain unclear. Here, we investigated the total and active microbial communities of stacked fermented grains of sauce-flavored Baijiu using flow cytometry and high-throughput sequencing technology, respectively. By using traditional high-throughput sequencing technology, a total of 24 bacterial and 14 fungal genera were identified as the core microbiota, the core bacteria were Lactobacillus (0.08–39.05%), Acetobacter (0.25–81.92%), Weissella (0.03–29.61%), etc. The core fungi were Issatchenkia (23.11–98.21%), Monascus (0.02–26.36%), Pichia (0.33–37.56%), etc. In contrast, using flow cytometry combined with high-throughput sequencing, the active dominant bacterial genera after cell sorting were found to be Herbaspirillum, Chitinophaga, Ralstonia, Phenylobacterium, Mucilaginibacter, and Bradyrhizobium, etc., whereas the active dominant fungal genera detected were Aspergillus, Pichia, Exophiala, Candelabrochaete, Italiomyces, and Papiliotrema, etc. These results indicate that although the abundance of Acetobacter, Monascus, and Issatchenkia was high after stacked fermentation, they may have little biological activity. Flow cytometry and cell sorting techniques have been used in the study of beer and wine, but exploring the microbiome in such a complex environment as Chinese baijiu has not been reported. The results also reveal that flow cytometry and cell sorting are convenient methods for rapidly monitoring complex microbial flora and can assist in exploring complex environmental samples.

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Section: Introductionmentioning

confidence: 99%

Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting

et al. 2023

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“…Bacterial probiotic strains are commonly from the genera Bacillus , Bifidobacterium , Lactobacillus , and Streptococcus ( Holzapfel et al 2001 , Fijan 2014 ). Because next-generation sequencing is gradually becoming less expensive, whole-genome-sequence (WGS)-based probiotic genome comparison has emerged as the predominant method for analyzing food and feed safety ( Koirala and Anal 2021 , Syromyatnikov et al 2022 ). Consequently, researchers have an increasing demand for a user-friendly platform that facilitates comprehensive whole-genome analyses of probiotics.…”

Section: Introductionmentioning

confidence: 99%

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains

Liu,

Hsu,

Yang

et al. 2023

Bioinformatics Advances

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Motivation ProbioMinServer is a platform designed to help researchers access information on probiotics regarding a wide variety of characteristics, such as safety (e.g., antimicrobial resistance, virulence, pathogenic, plasmid and prophage genes) and functionality (e.g., functional classes, carbohydrate-active enzyme, and metabolite gene cluster profile). Because probiotics are functional foods, their safety and functionality are a crucial part of health care. Genomics has become a crucial methodology for investigating the safety and functionality of probiotics in food and feed. This shift is primarily attributed to the growing affordability of next-generation sequencing technologies. However, no integrated platform is available for simultaneously evaluating probiotic strain safety, investigating probiotic functionality, and identifying known phylogenetically related strains. Results Thus, we constructed a new platform, ProbioMinServer, which incorporates these functions. ProbioMinServer accepts whole-genome sequence files in the FASTA format. If the query genome belongs to the 25 common probiotic species collected in our database, the server performs a database search and analyzes the core-genome multilocus sequence typing (cgMLST). Front-end applications were implemented in JavaScript with a bootstrap framework, and back-end programs were implemented using PHP, Perl, and Python. ProbioMinServer can help researchers quickly and easily retrieve information on the safety and functionality of various probiotics. Availability The platform is available at https://probiomindb.imst.nsysu.edu.tw. Supplementary information Supplementary data are available at Bioinformatics Advances online.

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Characterization and Authentication of Probiotic Preparations

Kothari

Souza²,

Mehta³

2023

Probiotics, Prebiotics, Synbiotics, and Postbiotics

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Probiotics analysis by high-throughput sequencing revealed multiple mismatches at bacteria genus level with the declared and actual composition

Cited by 8 publications

References 43 publications

Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting

Exploration of microbiome diversity of stacked fermented grains by flow cytometry and cell sorting

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains

Characterization and Authentication of Probiotic Preparations

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