Research Article

YS Flora®, a Comprehensive and Multi-Purpose Collection of Human Gut Microbiome

Minyoung Hong1, Sooyoon Cho1, Kyoung Jin Choi2,3, Gwanghee Kim1, Sang Sun Yoon1,2,3,4,5,*
Author Information & Copyright
1BioMe Inc. Seoul 02455, Korea
2Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 03722, Korea
3Brain Korea 21 Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Korea
4Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Korea
5Institute of Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
*Corresponding author : Sang Sun Yoon, BioMe Inc., 117-3 Heogi-ro, Dongdaemun-gu, Seoul 02455, Korea. Tel: +82-2-2228-1824, Fax: +82-2-392-7088, E-mail:

Copyright © Korean Society for Lactic Acid Bacteria and Probiotics. This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Received: Jul 31, 2023; Revised: Nov 27, 2023; Accepted: Dec 20, 2023

Published Online: Dec 31, 2023


Human feces, as a repository of the gut microbiome composed of tens of trillions of microbes, represent the microbial environment within the gut. The composition of the gut microbiota is associated with various diseases, body conditions, and lifestyles, and human-derived strains isolated from feces can be developed into probiotics or live biotherapeutic products (LBPs). YS Flora® is a collection of human fecal samples from over 300 diverse donors intended for scientific research and healthcare purposes, such as studying gut microbiome communities and developing supplements and pharmaceuticals. YS Flora® uniquely includes fecal samples from non-healthy individuals, unlike other fecal biobanks, to gain a comprehensive understanding of the human gut microbiome. To demonstrate YS Flora®’s utility for scientific research, we analyzed and compared the fecal bacterial communities of vegetarians and omnivores. Strains with potential for use as probiotics or LBPs, such as Lactobacillus spp., Bifidobacterium spp., and Bacillus spp., were isolated using selective media. YS Flora® provides a research foundation by offering isolated strains and gut microbiota from individuals with specific health conditions and lifestyles, enhancing the scientific understanding of the human gut microbiome and aiding researchers in developing probiotics or LBPs.

Keywords: human feces; gut microbiota; probiotics; live-biotherapeutic product; community analysis


The human gut hosts the largest scale of symbiotic microorganisms in the body, among which the bacterial population reaches up to one hundred billion per milliliter in the colon (Sender et al., 2016). The intestine contains bacteria such as Streptococcus, Lactobacillus, Bacteroides, Bifidobacterium, and Akkermansia, with the number of species amounting to 1,952 uncultured bacteria and 553 known colonizers (Almeida et al., 2019).

Certain microbes isolated from the intestines of healthy individuals are being developed into pharmaceuticals, targeting conditions such as gastrointestinal disorders, dental disorders, and conditions in infants (Cordaillat-Simmons et al., 2020). Traditional therapeutic approaches have encountered challenges, including mounting antibiotic and chemotherapy resistance, drug non-responsiveness, and limited specificity. In contrast, microbiome-based treatments offer promising solutions, as they surmount these limitations (Yadav and Chauhan, 2022).

Research results are being published indicating that the balance of intestinal microbial communities is closely interconnected with diseases. The composition of the gut microbiome is associated with the potential development of various conditions, including cancer (Tilg et al., 2018), autoimmune diseases (De Luca and Shoenfeld, 2019), metabolic syndrome (Fan and Pedersen, 2021), inflammatory bowel disease (Glassner et al., 2020), and neurodegenerative diseases (Zhu et al., 2021), by influencing gut permeability and mucosal immunity (Zheng et al., 2020). Next-generation sequencing has been utilized for the analysis of gut microbiomes, revealing correlations between microorganisms and diseases. It has been observed that dysbiosis are accompanied by decreased species richness and specific reductions in microbial taxa such as Ruminococcaceae and Lactobacillus, while Proteobacteria exhibit an increase (Zheng et al., 2020). The presence of certain microbes and their positive correlation with the occurrence and severity of specific diseases, for example, Escherichia coli and Ruminococcus gnavus in inflammatory bowel disease or Anaerotruncus colihominis, Lachnospira perfectinoschiza, and Ruminococcus callidus in cases of bloating and abdominal pain, suggests the potential use of microbes as bacterial biomarkers for disease diagnosis (Companys et al., 2021; Zhang et al., 2015).

Comprehensive fecal collection is important for multiple purposes, such as individual-specific gut microbiome community research and isolation of beneficial bacteria for the development of probiotics for animals or humans. Typical stool banks intended for fecal microbiota transplantation (FMT) primarily consist of fecal samples from healthy donors (Barnes and Park, 2017), restricting the diversity of intestinal microbial compositions available for research and medical purposes. In contrast, YS Flora® collected fecal samples from both healthy and non-healthy individuals, aiming to gain a more comprehensive understanding of the relationship between gut microbiome communities, diseases, and lifestyles. We collected fecal samples and corresponding information on physical conditions and lifestyles from over 300 donors and named this collection YS Flora®. To demonstrate the application of community analysis of YS Flora® fecal samples, we compared gut microbial communities between vegetarian and omnivorous dietary habits. Additionally, numerous beneficial bacteria with probiotic potential were isolated using selective media. YS Flora® aims to expand knowledge on the gut microbiome and contribute to human health as a multi-purpose collection of human feces and gut microbiome.

Materials and Methods

Organizing information on donor’s sample

The fecal collection process was conducted with approval from the Public Institutional Review Board (permission number P01-202306-06-001). Collection papers, tubes, consent forms, and questionnaires were distributed nationwide. For children, consent forms and questionnaires were adjusted to their appropriate level of understanding. Additionally, the questionnaire data was organized in our spreadsheet, which can be provided individually upon request. When categorizing the medication status of donors, we employed the drug classification criteria outlined by the Ministry of Food and Drug Safety (MFDS) of South Korea. Body mass index (BMI) was classified into underweight (< 18.5), normal weight (18.5~24.9), overweight (25.0~29.9), and obesity (30 ≤) categories based on the criteria of the World Health Organization.

For long-term storage, the fecal samples were suspended in glycerol. A sterilized solution of 25% glycerol and 0.9% NaCl (GS solution) was individually autoclaved at 121°C for 15 minutes and then combined. Subsequently, 1 g of feces was suspended in 9 mL of the GS solution, vigorously mixed, and frozen at –80°C.

Selection of feces for microbial community analysis

Six vegetarians and six omnivores were selected from the pool of donors, as dietary habits have been identified as one of the key factors influencing the composition of the intestinal microbial community. Fecal samples were primarily obtained from donors who did not consume probiotics or medications.

Creating and sequencing the Illumina MiSeq library

DNA extraction from the fecal samples of vegetarians and omnivores was carried out using the PowerSoil® DNA Isolation Kit (Qiagen, CA, USA). The V3-V4 region of the bacterial 16S rDNA was then amplified for subsequent amplicon sequencing, with the extracted DNA serving as the template. PCR was performed using specific primers designed for the DNA region (Forward: 5’-TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG CCT ACG GGN GGC WGC AG-3’; Reverse: 5’-GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GGA CTA CHV GGG TAT CTA ATC C-3’).

For PCR amplification, a PCR master mix was prepared by combining 12.5 ng of DNA, 1 μM of forward and reverse primers (5 μL each), and 2x KAPA HiFi HotStart Ready Mix (12.5 μL). PCR was conducted under the following conditions: initial denaturation at 95°C for 3 minutes, followed by 25 cycles of denaturation at 95°C for 30 seconds, annealing at 55°C for 30 seconds, elongation at 72°C for 30 seconds, and a final elongation step at 72°C for 5 minutes. The PCR products were purified using AMPure XP beads to remove residual primers and primer dimers.

The purified V3-V4 region amplicon (5 μL) was combined with the Nextera® XT Index Kit to construct the final sequencing library. This involved mounting the sample in a TruSeq Index Plate fixture and adding 5 μL of Index 1 and Index 2 primers from the Nextera XT Index Kit. Subsequently, the second PCR was performed using 2x KAPA HiFi HotStart Ready Mix (25 μL) and PCR Grade Water (10 μL), with the cycle count adjusted to 8 cycles for indexing the DNA library. The index-added V3-V4 region PCR amplicon was purified using AMPure XP beads.

The sample DNA libraries, combined with the attached indexes, were normalized using Qubit (Thermo Fisher Scientific, MA, USA) and Agilent 2100 Bioanalyzer (Agilent Technologies, CA, USA). Before cluster creation and sequencing, the DNA libraries underwent denaturation using sodium hydroxide, hybridization buffer, and the PhiX Control Kit. The sequencing was performed using MiSeq FGx (Illumina, CA, USA) equipment.

Diversity analysis of fecal microbial communities of each dietary group

In the amplicon sequencing results, the read files were processed using MiSeq Reporter software, Illumina’s on-instrument secondary analysis tool. Only sequences meeting the minimum base call quality criteria (Q30) were included for further analysis. The sequence data was then uploaded to the Quantitative Insights into Microbiological Ecology program and demultiplexed based on the tagging short index sequences.

To improve the accuracy of the reads, the Divisive Amplicon Denoising Algorithm 2 was employed for error calibration, and chimera sequences were removed. Subsequently, an amplicon sequence variant (ASV) feature table was generated. The bacterial identification for each ASV was conducted by referencing the 16S rRNA database from the National Center for Biotechnology Information.

Chao1 and Shannon’s indices were utilized to analyze alpha diversity. The beta diversity analysis involved the utilization of the Bray-Curtis dissimilarity metric, which was visualized using an unweighted-pair group method with an average linkage phylogenetic tree and principal coordinates analysis (PCoA) employing the weighted unifrac distance analysis method. A one-way analysis of similarities (ANOSIM) was conducted using the software R’s vegan package with a maximum of 999 permutations to assess the significance of dissimilarity between clusters. This analysis compared the similarity between vegetarians and carnivores in terms of global R and p-values.

Isolation and identification of bacterial strains

Bacteria widely recognized as beneficial, such as Lactobacillus and Bifidobacterium, were isolated from the fecal samples of the donors using selective media. Rogosa agar (Kisan Bio) and Bifidobacterium selective medium (BSM; Sigma) were employed to specifically isolate Lactobacillus spp. and Bifidobacterium spp., respectively. Medium supplements were added to the sterilized media separately.

Bacterial isolation was processed under aerobic or anaerobic conditions. The anaerobic condition in the anaerobic chamber (Vinyl type, Coy Laboratory Products, MI, USA) consisted of mixed gas with an N2:CO2:H2 ratio of 90:5:5. After serial dilution, 100 μL of fecal suspension was spread onto the reduced Rogosa and BSM agar plates and cultured anaerobically at 37°C for 48 hours. Bacillus species were isolated using the tryptic soy agar (TSA) medium under aerobic conditions at 37°C for 24 hours. Colonies with different morphologies were picked with sterile loops, then streaked on de Man, Rogosa, and Sharpe (MRS) agar containing 0.05% L-cysteine hydrochloride for Lactobacillus spp. or Bifidobacterium spp., or on TSA for Bacillus spp.

Polymerase chain reaction (PCR) was conducted to amplify 16S rRNA sequences and identify the individual isolated colonies. The DNA region with a length of 1,500 bp was amplified using the universal primer set 27F 5’-AGA GTT TGA TCC TGG CTC AG-3’ and 1492R 5’-GGT TAC CTT GTT ACG ACT T-3’. A single colony was picked and suspended in 100 μL of sterile water for colony PCR. A 30 μL reaction mixture consisting of 2X TOP simple Dye MIX-Tenuto PCR Prefix (20 μL), 10 pM forward and reverse primers (1 μL each), colony suspension (3 μL), and distilled water (5 μL) was prepared. PCR for 16S rRNA amplification composed of an initial denaturation step of 3 minutes at 94°C, followed by 30 cycles of 30 seconds at 94°C, 30 seconds at 58°C, and 2 minutes at 72°C. A final extension step of 10 minutes at 72°C was performed. The PCR product was purified using the Mini BEST DNA Fragment Purification Kit (TaKaRa Bio, Japan) and subsequently sequenced at Bionics (Korea).

Statistical analysis

All data calculations and statistical analyses were performed using GraphPad Prism ver. 9.4.1 (GraphPad Software Inc., CA, USA). Differences between groups were analyzed using one-way analysis of variance, and p values < 0.05 were considered statistically significant.


Acquisition of lifestyle and health-related information of feces donors

To ensure long-term storage, the feces were mixed with glycerol and frozen in a deep freezer. Based on age distribution, individuals in their 60s constituted the largest group, followed by those in their 50s (Fig. 1A). Regarding BMI, the majority (56%) fell into the normal weight (18.5~24.9) category. In comparison, only 8% were underweight (< 18.5), and 4% were classified as obese (30 ≤) category (Fig. 1B). In terms of caffeine and alcohol consumption, the majority of donors (60%) reported consuming less than one drink per week (Figs. 1C and 1D). Additionally, the number of individuals adhering to a vegetarian diet was 1.5 to 2 times higher than that of omnivores (Fig. 1E). An overwhelming majority (89%) reported defecating up to two times a day (Figs. 1F).

Fig. 1. Fecal donors’ information about lifestyles and health conditions. (A, B) Basic information on age and body mass index (BMI); (C-F) Lifestyle information, such as caffeine and alcohol intake, eating habits, and defecation frequency; (G-K) donors’ health conditions, such as stress levels, frequency of abdominal pain, diseases and/or disorders, types of medications, and nutritional supplements being taken.
Download Original Figure

Stress levels among donors were primarily reported as moderate or weaker (83%), and 78% experienced zero episodes of daily abdominal pain (Figs. 1G and 1H). Among the listed symptoms in Figure 1I, approximately 64% of the donors reported experiencing at least one of them, with hypertension being the most prevalent condition based on the questionnaire responses. Among the various types of drugs classified according to the drug classification system of the MFDS of Korea, circulatory system drugs were the most consumed (Fig. 1J). Furthermore, within the healthy and symptomatic donor groups, 56% reported taking antibiotic-containing drugs three months before fecal donation, and multivitamins were the most frequently consumed nutritional supplement (Fig. 1K).

Metagenome sequencing analysis of two distinct dietary groups

Research on the human gut microbiome community can be facilitated by utilizing fecal samples from YS Flora®. As an example, we conducted a metagenomic analysis and comparison of the gut microbiomes of donors following vegetarian and omnivorous diets. The sequencing depth for all samples exceeded 50,000 reads, with an average of 178,406 reads. After undergoing quality control, a total of 2,140,872 reads were obtained. The vegetarian group yielded a confirmed total of 1,092,614 reads, while the omnivore group had 1,048,258 reads. On average, each sample in the vegetarian group contained 182,102 reads, while the omnivore group had an average of 174,710 reads per sample. With an average Good’s coverage of 99.97%, the sequencing depth achieved by our read counts ensures a comprehensive capture of microbial diversity, indicating a high probability that we have sequenced the vast majority of species in our samples.

The alpha diversity analysis between the two dietary groups was represented by ASVs, Chao1 and Shannon indices (Figs. 2A-C). Statistical analysis revealed no significant difference in the average number of ASVs between the vegetarian and the omnivorous group. The Chao1 index, which reflects the number of unique ASVs in the community, showed a higher value in the vegetarian groups, although the difference was not statistically significant. The Shannon index, which measures microbial community diversity, showed a slight increase in the vegetarian group compared to the omnivore group, indicating greater diversity in individuals following a vegetable-oriented diet, but the difference did not reach statistical significance. To evaluate the similarity of bacteria composition between samples, we performed beta diversity analysis using the weighted unifrac method and visualized the results using PCoA (Fig. 2D). Microbiome compositions were found to be better maintained among vegetarians when compared to those of omnivores. The comparison using the Bray-Curtis similarity index and ANOSIM indicated that the differences in gut microbiota composition between the two groups were not statistically significant (global R = 0.02037, p = 0.3487).

Fig. 2. Diversity comparison between vegetarian and omnivore groups. (A-C) The amplicon sequence variants (ASVs), Chao1, and Shannon indices measured alpha diversity, and (D) beta diversity was analyzed by the Bray-Curtis dissimilarity measure and visualized by principal coordinate analysis (PCoA).
Download Original Figure

The composition of abundant species was compared between vegetarians and omnivores, resulting in a total of 372 species being analyzed. The microbiome compositional structures differ significantly between the two groups. The relative abundance at the species level was ranked in ascending order for the vegetarian group (Fig. 3). The top three species in the vegetarian group were Faecalibacterium prausnitzii, Phocaeicola vulgatus, and Blautia wexlerae. F. prausnitzii constituted an average of 7.5%, while the top three strains accounted for 18.4%. In the omnivore group, Pseudescherichia vulneris, Collinsella aerofaciens, and Blautia luti were found to be enriched. Ps. vulneris accounted for 7.9%, and the combined abundance of the top three strains was 13.7%.

Fig. 3. Relative abundance at the species level of vegetarian and omnivore groups. (V, vegetarian; O, omnivore).
Download Original Figure
The beneficial microbe isolates

To isolate specific strains of Lactobacillus spp. and Bifidobacterium spp., including those recognized for overall safety by the MFDS of Korea and other potentially beneficial strains for probiotic or pharmabiotic development, we utilized a fecal-glycerol suspension on two selective media and one basic medium. A total of 878 strains were isolated from the YS Flora®. Among them, 400 isolates belong to the species designated by the MFDS, meaning their overall safety is recognized and guaranteed by the Korean MFDS, allowing for their commercialization without additional safety evaluations (Table 1 and Supplementary Table S1). In addition to the MFDS-designated strains, a total of 405 species from which more than 10 isolates were obtained and which have been reported in research to have health-promoting or disease-curing functionalities are listed in Table 2. Bacillus spp. was predominantly isolated from the basic medium TSA. Lactic acid bacteria such as Lactobacillus spp., Weissella cibaria, Pediococcus spp., and Leuconostoc mesenteroides were primarily isolated from the Rogosa medium.

Table 1. Korean MFDS1)-designated species isolated from YS Flora®
Organism Isolation media Sum
BSM2) Rogosa TSA3)
Lactobacillus spp.
L. plantarum 8 63 - 71
L. paracasei 4 24 - 28
L. rhamnosus 3 19 - 22
L. salivarius 2 14 - 16
L. fermentum - 13 - 13
  L. gasseri - 6 - 6
L. acidophilus - 5 - 5
  L. casei - 4 - 4
  L. reuteri - 3 - 3
L. helveticus 1 - - 1
Bifidobacterium sp.
Bif. longum 31 - - 31
Lactococcus sp.
Lc. lactis - 1 2 3
Enterococcus spp.
E. faecium 122 6 27 155
E. faecalis 32 - 10 42

1) MFDS, Ministry of Food and Drug Safety;

2) BSM, Bifidobacterium selective medium;

3) TSA, tryptic soy agar.

Download Excel Table
Table 2. Isolates with health functional and/or disease-treating potentials
Organism Isolation media Sum
BSM1) Rogosa TSA2)
Bacillus spp.
B. subtilis 8 1 102 111
B. velezensis - - 18 18
B. methylotrophicus - - 14 14
Lactobacillus spp.
L. sakei 11 58 2 71
L. brevis - 21 1 22
Weissella sp.
W. cibaria 11 53 5 69
Pediococcus spp.
P. pentosaceus 6 22 1 29
P. acidilactici 1 12 - 13
Leuconostoc sp.
Leu. mesenteroides 1 36 1 38
Bifidobacterium sp.
Bif. pseudocatenulatum 20 - - 20

4) BSM, Bifidobacterium selective medium;

5) TSA, tryptic soy agar.

Download Excel Table


The main objective of this study was to advance the utilization of fecal collection YS Flora® for multiple applications, encompassing the isolation of microbes for the development of probiotics or live biotherapeutic products, as well as investigations into the composition of the gut microbiome. The donor information includes age, BMI, alcohol and caffeine consumption, dietary habits, stool frequency, stress level, abdominal pain, diseases, medication, and supplement (Figs. 1A-K), documented in our spreadsheet. YS Flora® provides a collection of fecal samples from a wide range of age groups, enabling analysis of various studies such as the age-related core microbiome composition and variations in short-chain fatty acid-producing bacteria (Odamaki et al., 2016). Moreover, YS Flora® is well-suited for comparing gut microbial communities between individuals with a healthy condition and those with 22 different diseases and disorders (Fig. 1I). Typical stool banks operating for FMT purposes select only a small percentage (less than 5%) of fecal samples from healthy donors after rigorous testing (He et al., 2021). In contrast, YS Flora®, not intended for FMT, has also secured fecal samples from non-healthy individuals. This approach allows insights into the associations between gut microbial composition and health conditions and lifestyles, such as stress levels, antibiotics usage, stomachaches, and diseases (De Vos et al., 2022).

The community analysis results of fecal samples from vegetarians and omnivores demonstrate that 16S rRNA metagenomic amplicon sequencing of YS Flora® fecal samples can be represented in terms of alpha or beta diversity and predominant species (Figs. 2A-D). Although this example did not show significant differences in alpha and beta diversity between vegetarian and omnivore feces, these are not always similar and can vary depending on nutrient intake, including carbohydrates, proteins, and fats, despite the contrasting diets or other factors such as age, sex, and BMI (Losasso et al., 2018; Matijašić et al., 2014; Ruengsomwong et al., 2016). In the analysis of dominant species within each dietary group, F. prausnitzii, P. vulgatus, and B. wexlerae were identified as the predominant species in the fecal samples of vegetarians, which aligns with previous studies where these species were commonly found in the feces of vegetarians and considered indicative of a vegetarian diet (Dridi et al., 2023; Ferrocino et al., 2015; Kjølbæk et al., 2020; Nakajima et al., 2020; Patnode et al., 2019; Takei et al., 2022; Xia et al., 2022; Zafar and Saier, 2021). On the other hand, among the abundant species in the fecal samples of the omnivore group, P. vulneris, C. aerofaciens, and B. luti were prominently observed. C. aerofaciens has been reported to be more prevalent in the non-vegetarian group and in individuals with low dietary fiber intake (Gomez-Arango et al., 2018; Ruengsomwong et al., 2016). However, further research is required to elucidate the reasons behind the higher abundance of P. vulneris, a microorganism widely distributed in different parts of the human body (Brenner et al., 1982), and B. luti, known for its ability to ferment carbohydrates (Kjølbæk et al., 2020), in the fecal samples of individuals following a meat-based diet.

Species identified as designated strains of MFDS and others, with more than 10 isolates from YS Flora® feces, with potential health benefits or disease healing properties based on literature research. The strains listed in Table 1 are considered relatively safe and can potentially be developed into probiotics and therapeutic agents based on their confirmed functionality without additional safety verification (Fijan, 2014). Over 400 strains with various potential functionalities have been secured (Table 2), among which Bacillus species have been reported to exhibit antimicrobial activity, antiviral effects, and toxin neutralization (Byun et al., 2023; Lee et al., 2019; Xie et al., 2023; Zhang et al., 2021). Lactobacillus sakei and Lactobacillus brevis have been studied for increasing beneficial microbial richness and abundance, metabolic regulation and anti-diabetic properties, anti-inflammatory effects, and immune regulation (Chen et al., 2023; Kwon et al., 2018; Riccia et al., 2007; Zou et al., 2023). Pediococcus strains have been reported for metabolic regulation, proliferation of beneficial microbes, and suppression of harmful pathogens (Al-Emran et al., 2022; Silva et al., 2017; Ueda et al., 2018). W. cibaria and Leu. mesenteroides have been found to improve oral health by reducing halitosis and inhibiting Streptococcus mutans, and to alleviate skin conditions such as psoriasis and atopic dermatitis (Lee et al., 2021; Lim et al., 2017; Luan et al., 2022; Ogawa et al., 2021). Bifidobacterium pseudocatenulatum has been studied for enhancing intestinal barrier function, reducing intestinal permeability, and consequently decreasing bacteria-induced inflammatory responses, such as in rheumatoid arthritis and cirrhosis (Moratalla et al., 2016; Zhao et al., 2023).

YS Flora® is a comprehensive collection of human feces from individuals with diverse lifestyles and physical conditions. This collection provides a representative sample of an individual’s intestinal microbial pool for multiple purposes, such as community analyses, and secures isolates of beneficial microbes. Further studies will evaluate the safety and efficacy of beneficial microbes derived from YS Flora® for specific indications. Furthermore, conducting community analyses with a larger sample size of fecal samples will contribute to expanding our knowledge of the relationship between gut microbiota, lifestyles, and diseases.


We express our gratitude to all the donors who voluntarily contributed their fecal samples and personal information for scientific research.

This work was supported by a grant of the Tech Incubator Program for Startup (TIPS) funded by the Ministry of SMEs and Startups, Republic of Korea (S3287890).



Al-Emran HM, Moon JF, Miah ML, Meghla NS, Reuben RC, Uddin MJ, Ibnat H, Sarkar SL, Roy PC, Rahman MS, Alam ASMRU, Islam OK and Jahid IK (2022) Genomic analysis and in vivo efficacy of Pediococcus acidilactici as a potential probiotic to prevent hyperglycemia, hypercholesterolemia and gastrointestinal infections. Scientific Reports, 12(1).


Almeida A, Mitchell AL, Boland M, Forster SC, Gloor GB, Tarkowska A, Lawley TD and Finn RD (2019) A new genomic blueprint of the human gut microbiota. Nature, 568(7753), 499–504.


Barnes D and Park KT (2017) Donor considerations in fecal microbiota transplantation. In Current Gastroenterology Reports (Vol. 19, Issue 3). Current Medicine Group LLC 1.


Brenner DJ, McWhorter AC, Knutson JK and Steigerwalt AG (1982) Escherichia vulneris: A new species of Enterobacteriaceae associated with human wounds. In Journal of Clinical Microbiology, 15(6).


Byun H, Brockett MR, Pu Q, Hrycko AJ, Beld J and Zhu J (2023) An intestinal Bacillus velezensis isolate displays broad-spectrum antibacterial activity and prevents infection of both gram-positive and gram-negative pathogens in vivo. Journal of Bacteriology, 205(6).


Chen S, Han P, Zhang Q, Liu P, Liu J, Zhao L, Guo L and Li J (2023) Lactobacillus brevis alleviates the progress of hepatocellular carcinoma and type 2 diabetes in mice model via interplay of gut microflora, bile acid and NOTCH 1 signaling. Frontiers in Immunology, 14.


Companys J, Gosalbes MJ, Pla-Pagà L, Calderón-Pérez L, Llauradó E, Pedret A, Valls RM, Jiménez-Hernández N, Sandoval-Ramirez BA, del Bas JM, Caimari A, Rubió L and Solà R (2021) Gut microbiota profile and its association with clinical variables and dietary intake in overweight/obese and lean subjects: A cross-sectional study. Nutrients, 13(6).


Cordaillat-Simmons M, Rouanet A and Pot B (2020) Live biotherapeutic products: The importance of a defined regulatory framework. In Experimental and Molecular Medicine (Vol. 52, Issue 9, pp. 1397–1406). Springer Nature.


De Luca F and Shoenfeld Y (2019) The microbiome in autoimmune diseases. In Clinical and Experimental Immunology (Vol. 195, Issue 1, pp. 74–85). Blackwell Publishing Ltd.


De Vos WM, Tilg H, Van Hul M and Cani PD (2022) Gut microbiome and health: Mechanistic insights. In Gut. BMJ Publishing Group.


Dridi L, Altamura F, Gonzalez E, Lui O, Kubinski R, Pidgeon R, Montagut A, Chong J, Xia J, Maurice CF and Castagner B (2023) Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting. Nature Communications, 14(1).


Fan Y and Pedersen O (2021) Gut microbiota in human metabolic health and disease. In Nature Reviews Microbiology (Vol. 19, Issue 1, pp. 55–71). Nature Research.


Ferrocino I, Di Cagno R, De Angelis M, Turroni S, Vannini L, Bancalari E, Rantsiou K, Cardinali G, Neviani E and Cocolin L (2015) Fecal microbiota in healthy subjects following omnivore, vegetarian and vegan diets: Culturable populations and rRNA DGGE profiling. PLoS ONE, 10(6).


Fijan S (2014) Microorganisms with claimed probiotic properties: An overview of recent literature. In International Journal of Environmental Research and Public Health (Vol. 11, Issue 5, pp. 4745–4767). MDPI.


Glassner KL, Abraham BP and Quigley EMM (2020) The microbiome and inflammatory bowel disease. Journal of Allergy and Clinical Immunology, 145(1), 16–27.


Gomez-Arango LF, Barrett HL, Wilkinson SA, Callaway LK, McIntyre HD, Morrison M and Dekker Nitert M (2018) Low dietary fiber intake increases Collinsella abundance in the gut microbiota of overweight and obese pregnant women. Gut Microbes, 9(3), 189–201.


He J, He X, Ma Y, Yang L, Fang H, Shang S, Xia H, Lian G, Tang H, Wang Q, Wang J, Lin Z, Wen J, Liu Y, Zhai C, Wang W, Jiang X, Xuan J, Liu M, Lu S, Li X, Wang H, Ouyang C, Cao M, Lin A, Zhang B, Wu D, Chen Y and Xiao C (2021) A comprehensive approach to stool donor screening for faecal microbiota transplantation in China. Microbial Cell Factories, 20(1).


Kjølbæk L, Benítez-Páez A, Gómez del Pulgar EM, Brahe LK, Liebisch G, Matysik S, Rampelli S, Vermeiren J, Brigidi P, Larsen LH, Astrup A and Sanz Y (2020) Arabinoxylan oligosaccharides and polyunsaturated fatty acid effects on gut microbiota and metabolic markers in overweight individuals with signs of metabolic syndrome: A randomized cross-over trial. Clinical Nutrition, 39(1), 67–79.


Kwon MS, Lim SK, Jang JY, Lee J, Park HK, Kim N, Yun M, Shin MY, Jo HE, Oh YJ, Roh SW and Choi HJ (2018) Lactobacillus sakei WIKIM30 ameliorates atopic dermatitis-like skin lesions by inducing regulatory T cells and altering gut microbiota structure in mice. Frontiers in Immunology, 9(AUG).


Lee DS, Kim M, Nam SH, Kang MS and Lee SA (2021) Effects of oral probiotics on subjective halitosis, oral health, and psychosocial health of college students: A randomized, double-blind, placebo-controlled study. International Journal of Environmental Research and Public Health, 18(3), 1–10.


Lee NK, Kim WS and Paik HD (2019) Bacillus strains as human probiotics: characterization, safety, microbiome, and probiotic carrier. In Food Science and Biotechnology (Vol. 28, Issue 5, pp. 1297–1305). The Korean Society of Food Science and Technology.


Lim SK, Kwon MS, Lee J, Oh YJ, Jang JY, Lee JH, Park HW, Nam YDo, Seo MJ, Roh SW and Choi HJ (2017) Weissella cibaria WIKIM28 ameliorates atopic dermatitis-like skin lesions by inducing tolerogenic dendritic cells and regulatory T cells in BALB/c mice. Scientific Reports, 7.


Losasso C, Eckert EM, Mastrorilli E, Villiger J, Mancin M, Patuzzi I, Di Cesare A, Cibin V, Barrucci F, Pernthaler J, Corno G and Ricci A (2018) Assessing the influence of vegan, vegetarian and omnivore oriented westernized dietary styles on human gut microbiota: A cross sectional study. Frontiers in Microbiology, 9(MAR).


Luan C, Yan J, Jiang N, Zhang C, Geng X, Li Z and Li C (2022) Leuconostoc mesenteroides LVBH107 antibacterial activity against Porphyromonas gingivalis and anti-Inflammatory Activity against P. gingivalis lipopolysaccharide-stimulated RAW 264.7 cells. Nutrients, 14(13).


Matijašić BB, Obermajer T, Lipoglavšek L, Grabnar I, Avguštin G and Rogelj I (2014) Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia. European Journal of Nutrition, 53(4), 1051–1064.


Moratalla A, Gómez-Hurtado I, Moya-Pérez Á, Zapater P, Peiró G, González-Navajas JM, Gómez Del Pulgar EM, Such J, Sanz Y and Francés R (2016) Bifidobacterium pseudocatenulatum CECT7765 promotes a TLR2-dependent anti-inflammatory response in intestinal lymphocytes from mice with cirrhosis. European Journal of Nutrition, 55(1), 197–206.


Nakajima A, Sasaki T, Itoh K, Kitahara T, Takema Y, Hiramatsu K, Ishikawa D, Shibuya T, Kobayashi O, Osada T, Watanabe S and Nagahara A (2020) A soluble fiber diet increases Bacteroides fragilis group abundance and immunoglobulin a production in the gut. Applied and Environmental Microbiology, 86(13), e00405-20.


Odamaki T, Kato K, Sugahara H, Hashikura N, Takahashi S, Xiao JZ, Abe F and Osawa R (2016) Age-related changes in gut microbiota composition from newborn to centenarian: A cross-sectional study. BMC Microbiology, 16(1).


Ogawa C, Inoue R, Yonejima Y, Hisa K, Yamamoto Y and Suzuki T (2021) Supplemental Leuconostoc mesenteroides strain NTM048 attenuates imiquimod-induced psoriasis in mice. Journal of Applied Microbiology, 131(6), 3043–3055.


Patnode ML, Beller ZW, Han ND, Cheng J, Peters SL, Terrapon N, Henrissat B, Le Gall S, Saulnier L, Hayashi DK, Meynier A, Vinoy S, Giannone RJ, Hettich RL and Gordon JI (2019) Interspecies competition impacts targeted manipulation of human gut bacteria by fiber-derived glycans. Cell, 179(1), 59-73.e13.


Riccia DND, Bizzini F, Perilli MG, Polimeni A, Trinchieri V, Amicosante G and Cifone MG (2007) Anti-inflammatory effects of Lactobacillusbrevis (CD2) on periodontal disease. Oral Diseases, 13(4), 376–385.


Ruengsomwong S, La-Ongkham O, Jiang J, Wannissorn B, Nakayama J and Nitisinprasert S (2016) Microbial community of healthy thai vegetarians and non-vegetarians, their core gut microbiota, and pathogen risk. Journal of Microbiology and Biotechnology, 26(10), 1723–1735.


Sender R, Fuchs S and Milo R (2016) Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14(8).


Silva BC, Sandes SHC, Alvim LB, Bomfim MRQ, Nicoli JR, Neumann E and Nunes AC (2017) Selection of a candidate probiotic strain of Pediococcus pentosaceus from the faecal microbiota of horses by in vitro testing and health claims in a mouse model of Salmonella infection. Journal of Applied Microbiology, 122(1), 225–238.


Takei N, Kuda T, Handa N, Takahashi H and Kimura B (2022) Detection and isolation of typical gut indigenous bacteria in mice fed corn starch, bread flour or whole wheat flour. Food Bioengineering, 1(1), 91–100.


Tilg H, Adolph TE, Gerner RR and Moschen AR (2018) The intestinal microbiota in colorectal cancer. In Cancer Cell (Vol. 33, Issue 6, pp. 954–964). Cell Press.


Ueda T, Tategaki A, Hamada K, Kishida H, Hosoe K, Morikawa H and Nakagawa K (2018) Effects of pediococcus acidilactici r037 on serum triglyceride levels in mice and rats after oral administration. In J. Nutr. Sci. Vitaminol, 64.


Xia Y, Lee G, Yamamoto M, Takahashi H and Kuda T (2022) Detection of indigenous gut bacteria related to red chilli pepper (Capsicum annuum) in murine caecum and human faecal cultures. Molecular Biology. Reports, 49(11), 10239–10250.


Xie Y, Chupina Estrada A, Nelson B, Feng H, Pothoulakis C, Chesnel L and Koon HW (2023) ADS024, a Bacillus velezensis strain, protects human colonic epithelial cells against C. difficile toxin-mediated apoptosis. Frontiers in Microbiology, 13.


Yadav M and Chauhan NS (2022) Microbiome therapeutics: Exploring the present scenario and challenges. In Gastroenterology Report (Vol. 10). Oxford University Press.


Zafar H and Saier MH (2021). Gut Bacteroides species in health and disease. In Gut Microbes (Vol. 13, Issue 1, pp. 1–20). Bellwether Publishing, Ltd.


Zhang F, Wang B, Liu S, Chen Y, Lin Y, Liu Z, Zhang X and Yu B (2021) Bacillus subtilis revives conventional antibiotics against Staphylococcus aureus osteomyelitis. Microbial Cell Factories, 20(1).


Zhang YJ, Li S, Gan RY, Zhou T, Xu DP and Li H (2015) Impacts of gut bacteria on human health and diseases. In International Journal of Molecular Sciences (Vol. 16, Issue 4, pp. 7493–7519). MDPI AG.


Zhao Q, Ren H, Yang N, Xia X, Chen Q, Zhou D, Liu Z, Chen X, Chen Y, Huang W, Zhou H, Xu H and Zhang W (2023) Bifidobacterium pseudocatenulatum-mediated bile acid metabolism to prevent rheumatoid arthritis via the gut–joint axis. Nutrients, 15(2).


Zheng D, Liwinski T and Elinav E (2020) Interaction between microbiota and immunity in health and disease. In Cell Research (Vol. 30, Issue 6, pp. 492–506). Springer Nature.


Zhu X, Li B, Lou P, Dai T, Chen Y, Zhuge A, Yuan Y and Li L (2021) The relationship between the gut microbiome and neurodegenerative diseases. Neuroscience Bulletin, 37(10), 1510–1522.


Zou X, Pan L, Xu M, Wang X, Wang Q and Han Y (2023) Probiotic potential of Lactobacillus sakei L-7 in regulating gut microbiota and metabolism. Microbiological Research, 274, 127438.


Supplementary Table 1. A list of species designated by the Ministry of Food and Drug Safety of South Korea
Genus Species and subspecies
Lactobacillus L. acidophilus
L. casei
L. delbrueckii ssp. bulgaricus
L. gasseri
L. helveticus
L. fermentum
L. paracasei
L. plantarum
L. reuteri
L. rhamnosus
L. salivarius
Bifidobacterium Bif. animalis ssp. lactis
Bif. bifidum
Bif. breve
Bif. longum
Lactococcus Lc. lactis
Streptococcus S. thermophilus
Enterococcus E. faecalis
E. faecium
Download Excel Table