Genotyping by PCR and high-throughput sequencing of commercial probiotic products reveals composition biases
Open accessAbstract
Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation “well defined strains,” encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species, and determined their content using plate counting, targeted genotyping. Additionally, strain identities were assessed using methods recently published by the United States Pharmacopeial Convention. We also determined the relative abundance of individual bacteria by high-throughput sequencing (HTS) of the 16S rRNA sequence using paired-end 2x250bp Illumina MiSeq technology. Using multiple methods, we tested the hypothesis that products do contain the quantitative amount of labeled bacteria, and qualitative list of labeled microbial species. We found that 17 samples (33%) were below label claim for CFU prior to their expiration dates. A multiplexed-PCR scheme showed that only 30/52 (58%) of the products contained a correctly labeled classification, with issues encompassing incorrect taxonomy, missing species and un-labeled species. The HTS revealed that many blended products consisted predominantly of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis. These results highlight the need for reliable methods to qualitatively determine the correct taxonomy and quantitatively ascertain the relative amounts of mixed microbial populations in commercial probiotic products.
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Global assessments report label-claim discrepancies in over 40% of commercial probiotics.
“These findings align with global assessments, which report label-claim discrepancies in over 40% of commercial probiotics.24,25”
From Safety and efficacy concerns in Indian probiotics: Insights from whole-genome sequencing and <i>in vitro</i> assessment (2026) · cites this paper as [25]
The Results section reports labeling discrepancies in 22 of 52 tested products (42.3%), supporting the ‘over 40%’ figure. But the Materials and methods section says the products were purchased from retailers in Madison, Wisconsin; this study does not establish a global rate of discrepancies. (LLM, conf=0.88)
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Ladero, V., & Sánchez, B. (2017) · Current Opinion in Food Science · doi:10.1016/j.cofs.2017.03.002 · Cited by 22 · see citing works
Kim, H.-B., Kim, E., Yang, S.-M., Lee, S.-Y., Kim, M., & Kim, H. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.02087 · Cited by 22 · see citing works
Probiotic properties of Lactobacillus plantarum and application in prebiotic gummies
Feng, S., Wang, H., Lin, X., Liang, H., Zhang, S., Chen, Y., & Ji, C. (2022) · LWT · doi:10.1016/j.lwt.2022.114357 · Cited by 21 · see citing works
Kim, E., Kim, H.-B., Yang, S.-M., Kim, D., & Kim, H.-Y. (2020) · LWT · doi:10.1016/j.lwt.2020.110789 · Cited by 19 · see citing works
Unveiling The Therapeutic Potential of Probiotics: A Review
Tukaram, K. S., Sopanrao, S. R., & Kacharu, L. O. (2025) · Journal of Future Foods · doi:10.1016/j.jfutfo.2025.09.011 · Cited by 19 · see citing works
Alemu, B. K., Wu, L., Gedefaw, G. A., Lau, S. L., Wang, Y., & Wang, C. C. (2024) · Journal of Global Health · doi:10.7189/jogh.14.04177 · Cited by 20 · see citing works
“Through the process of genotyping with a high throughput sequencing method such as metagenomic analysis revealed that Lactobacillus and Bifidobacterium bacteria constituted most of the composition within the products [61,62].”
MethodShehata, H. R., & Newmaster, S. G. (2020) · Journal of AOAC International · doi:10.1093/jaoacint/qsaa063 · Cited by 17 · see citing works
Jordan, C. R., Harris, C. M., Miranda, M. I., Kim, D. Y., & Hellberg, R. S. R. (2023) · Food Control · doi:10.1016/j.foodcont.2023.109673 · Cited by 17 · see citing works
“The compounds in vacha have been associated with a variety of health-promoting properties (Olas & Bryś, 2018), including some animal-based studies suggesting antidiarrheal and antispasmodic activity (Mukherjee et al., 2007).”
Shehata, H. R., & Newmaster, S. G. (2021) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-021-09849-6 · Cited by 16 · see citing works
Ren, Y. N., Zheng, Y., Wang, X., Qu, S., Sun, L., Song, C., Ding, J. J., Ji, Y., Wang, G., Zhu, P., et al. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1361180 · Cited by 16 · see citing works
“…alpha subunit, β -tubulin, and calmodulin), genome-wide single-nucleotide polymorphisms (SNPs), multilocus sequence typing (either core genome or whole-genome), or amplified fragment length polymorphism (Keith and Jolley, 2014; Mareike et al., 2014; Morovic et al., 2016; Lugli et al., 2019).”
BackgroundPierro, F. D., Polzonetti, V., Patrone, V., & Morelli, L. (2019) · Microorganisms · doi:10.3390/microorganisms7110524 · Cited by 16 · see citing works
Microbiome's Universe: Impact on health, disease and cancer treatment
Réthi‐Nagy, Z., & Juhász, S. (2024) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2024.07.002 · Cited by 16 · see citing works
Syromyatnikov, M., Nesterova, E. Y., Gladkikh, M. I., & Popov, V. N. (2022) · LWT · doi:10.1016/j.lwt.2021.113055 · Cited by 14 · see citing works
Castagliuolo, I., Scarpa, M., Brun, P., Bernabé, G., Sagheddu, V., Elli, M., Fiore, W., Vitis, V. D., & Guglielmetti, S. (2021) · Annals of Microbiology · doi:10.1186/s13213-021-01655-3 · Cited by 14 · see citing works
Shehata, H. R., Ragupathy, S., Allen, S., Leyer, G. J., & Newmaster, S. G. (2020) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-020-09695-y · Cited by 13 · see citing works
“Maintaining cell viability throughout shelf life is known to be a challenge for industry [5] since it is affected by many environmental factors [6].”
BackgroundThe power of DNA based methods in probiotic authentication
Shehata, H. R., & Newmaster, S. G. (2023) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1158440 · Cited by 12 · see citing works
“DNA based methods include targeted methods (species-specific and strain-specific PCR methods) and non-targeted methods (e.g., high-throughput sequencing, HTS; Fasoli et al., 2003; Theunissen et al., 2005; Marcobal et al., 2008; Drago et al., 2010; Simmons et al., 2015; Morovic et al., 2016; Patro et al., 2016; Chen et…”
BackgroundMethodInfluentialMohr, A., Pyne, D., Leite, G., Akins, D., & Pugh, J. (2022) · Journal of Sport and Health Science · doi:10.1016/j.jshs.2022.12.012 · Cited by 12 · see citing works
“63 Enhancing storage conditions using specialized containment, working with the manufacturer to get viable count data at the time of production, adhering to a reasonable study length for product stability (i.e., shelf-life), and providing information to participants on best practices for the…”
MethodValletta, M., Campolattano, N., Chiara, I. D., Marasco, R., Singh, V. P., Muscariello, L., Pedone, P. V., Chambery, A., & Russo, R. (2023) · Food Research International · doi:10.1016/j.foodres.2023.113298 · Cited by 11 · see citing works
Compositional Quality and Possible Gastrointestinal Performance of Marketed Probiotic Supplements
Aziz, G., Zaidi, A., & Tariq, M. (2022) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-022-09931-7 · Cited by 11 · see citing works
Forssten, S. D., Morovic, W., & Nurminen, P. H. (2023) · Poultry Science · doi:10.1016/j.psj.2023.102654 · Cited by 11 · see citing works
Self-citationProbiotics and Their Quality-Related Concerns: Highlights From the Saudi Arabian Market
Aldawsari, F. S., Binhelel, B. S., Alshehri, Y. M., Alharbi, Y. T., & Abudahash, M. A. (2020) · Therapeutic Innovation & Regulatory Science · doi:10.1007/s43441-019-00064-8 · Cited by 11 · see citing works
“Nevertheless, there were reported cases in which as many as 46% of the tested probiotics revealed fewer viable microbes than the labeling stated.(16,17) Previously, SFDA laboratories have identified cases in which some probiotics contained only 50% of the label claim or did not contain live microbes at all (unpublishe…”
BackgroundLi, Y., Fan, B., Li, D., et al. (2020) · Aquaculture Reports · doi:10.1016/j.aqrep.2020.100548 · Cited by 11 · see citing works
Berezhnaya, Y., Bikaeva, I., Gachkovskaia, A., et al. (2021) · LWT · doi:10.1016/j.lwt.2021.111750 · Cited by 11 · see citing works
Foley, M. H., McMillan, A. S., O’Flaherty, S., Thanissery, R., Vanhoy, M. E., Fuller, M. G., Barrangou, R., & Theriot, C. M. (2025) · mBio · doi:10.1128/mbio.01468-25 · Cited by 10 · see citing works
“L. acidophilus NCFM and L. gasseri Lg-36 were selected as model probiotic strains to test due to the wide use and inclusion of these species in common probiotic formulations and their use to modulate CDI in pre-clinical and clinical trials (36, 60–63).”
Self-citationShehata, H. R., Kiefer, A., Morovic, W., & Newmaster, S. G. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.801795 · Cited by 10 · see citing works
“Methodologies have been developed for the identification of several probiotic species and strains (Solano-Aguilar et al., 2008; Ahlroos and Tynkkynen, 2009; Achilleos and Berthier, 2013; Herbel et al., 2013; Morovic et al., 2016; Shehata et al., 2020; Shehata and Newmaster, 2020a).”
BackgroundSelf-citationQualidade e viabilidade de probióticos comercializados em farmácias magistrais de Cascavel-PR
da Silva, E. C. D. S. H., & Bender, S. (2021) · Research Society and Development · doi:10.33448/rsd-v10i14.21822 · Cited by 8 · see citing works
Fernández, L., Orgaz, B., & Rodríguez, J. M. (2024) · Foods · doi:10.3390/foods13244024 · Cited by 8 · see citing works
Quality challenges associated with microbial-based cleaning products from the Industry Perspective
Teasdale, S. M., & Kademi, A. (2017) · Food and Chemical Toxicology · doi:10.1016/j.fct.2017.10.029 · Cited by 8 · see citing works
Shin, J., Chung, W., Park, Y.-S., & Nam, Y. (2022) · LWT · doi:10.1016/j.lwt.2022.114166 · Cited by 7 · see citing works
Song, Z., Ge, Y., Yu, X., Liu, R., Liu, C., Cheng, K., Guo, L., & Yao, S. (2024) · Journal of Dairy Science · doi:10.3168/jds.2023-23655 · Cited by 6 · see citing works
“Culture-based methods are commonly used to identify probiotic species/strains, but they provide relatively low taxonomic resolution(Morovic et al., 2016).”
MethodBautista, N. B., Dumancas, G. G., Ubas, J. G., Bandeling, E. J. D., Seduco, R. A. C., Martizano, J. O., & Janagap, S. P. (2023) · Journal of Agricultural and Food Chemistry · doi:10.1021/acs.jafc.3c04766 · Cited by 6 · see citing works
Kim, E., Kim, D., Yang, S.-M., & Kim, H. (2022) · Microbiological Research · doi:10.1016/j.micres.2022.127013 · Cited by 6 · see citing works
Rashid, Z., Gilani, S. M. H., Ashraf, A., Zehra, S., Azhar, A., Al‐Ghanim, K. A., Al-Misned, F. A., Mahboob, S., & Galani, S. (2019) · Journal of King Saud University - Science · doi:10.1016/j.jksus.2019.09.013 · Cited by 6 · see citing works
Shehata, H. R., & Newmaster, S. G. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-817242-1.00011-7 · Cited by 6 · see citing works
Bovine Liver Supplement Labeling Practices and Compliance With U.S. Regulations
Silva, A. J., Dahm, O. J., & Hellberg, R. S. R. (2020) · Journal of Dietary Supplements · doi:10.1080/19390211.2020.1834048 · Cited by 5 · see citing works
“Previous studies have reported mislabeling of dietary supplements, including shark cartilage (Isaacs and Hellberg 2019), probiotic supplements (Morovic et al. 2016), and herbal products (Newmaster et al.”
BackgroundDahm, O. J., Sampson, G. L., Silva, A. J., & Hellberg, R. S. R. (2021) · Journal of Dietary Supplements · doi:10.1080/19390211.2021.1887424 · Cited by 4 · see citing works
“2019), as well as probiotics that don’t meet label claim or detection thresholds for strains listed on the label (Morovic et al. 2016).”
BackgroundResultInfluentialNanobodies as potential tools for microbiological testing of live biotherapeutic products
Dorosky, R. J., Schreier, J. E., Lola, S. L., Sava, R. L., Coryell, M. P., Akue, A. D., KuKuruga, M. A., Carlson, P. E., Dreher‐Lesnick, S. M., & Stibitz, S. (2024) · AMB Express · doi:10.1186/s13568-023-01659-z · Cited by 4 · see citing works
“Molecular methods to evaluate potency of probiotic product powders and suspensions by sequencing techniques and PCR assays have been described (Hansen et al. 2018; Kiefer et al. 2020; Morovic et al. 2016; Patro et al. 2016).”
MethodRecent Research Technologies for Quality Control of Commercial Probiotics
Kim, B. (2019) · Current Topic in Lactic Acid Bacteria and Probiotics · doi:10.35732/ctlabp.2019.5.2.39 · Cited by 4 · see citing works
“가령, 제품내에 표기된 최소 균주 함유량에 미달하는 사례, 미생물의 동정이 잘못되어 있는 사례, 제품내에 표기되어 있지 않은 균주의 오염 사례 등이다 (Morovic et al., 2016).”
Occurrence and applications of CRISPR-Cas systems in bifidobacteria
Shin, J., & Barrangou, R. (2026) · Applied and Environmental Microbiology · doi:10.1128/aem.01703-25 · Cited by 4 · see citing works
Self-citationMetagenomics for the identification and characterization of microorganisms in fermented foods
Gbashi, S., Tebele, S. M., & Njobeh, P. B. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-98341-9.00021-9 · Cited by 3 · see citing works
Authenticity of probiotic foods and supplements: Up-to-date situation and methods to assess it
Fusco, V., Fanelli, F., & Chieffi, D. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-89908-6.00015-7 · Cited by 3 · see citing works
Pan, M., O’Flaherty, S., Hibberd, A. A., Gerdes, S., Morovic, W., & Barrangou, R. (2025) · BMC Genomics · doi:10.1186/s12864-024-11177-2 · Cited by 2 · see citing works
“This is further exacerbated by some rampant issues in the dietary supplement industry, in which products are frequently mis-labeled, encompassing species and strain mis-identification, as well as viable cell count variability and shortcomings [22].”
Self-citationAziz, G., Zaidi, A., & Sullivan, D. J. (2023) · Current Genetics · doi:10.1007/s00294-023-01271-5 · Cited by 2 · see citing works
“High-throughput sequencing by metagenomics is a quick and reliable approach to identify minute changes in probiotic strains (Mora et al. 2019; Patro et al. 2016; Ullah et al. 2019; Morovic et al. 2016; Lugli et al. 2019).”
BackgroundValidation and Optimization of qPCR Method for Identification of Actaea racemosa (Black Cohosh) NHPs
Shanmughanandhan, J., Shanmughanandhan, D., Ragupathy, S., et al. (2020) · Journal of AOAC International · doi:10.1093/jaoacint/qsaa167 · Cited by 2 · see citing works
Probiotics and Their Quality-Related Concerns: Highlights From the Saudi Arabian Market
Aldawsari, F. S., Binhelel, B. S., Alshehri, Y. M., Alharbi, Y. T., & Abudahash, M. A. (2019) · Therapeutic Innovation & Regulatory Science · doi:10.1177/2168479019841024 · Cited by 2 · see citing works
Shehata, H. R., Hassane, B., & Newmaster, S. G. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1360241 · Cited by 1 · see citing works
Development of reference-based model for improved analysis of bacterial community
Park, C., Park, J., Chang, D., & Kim, S. (2025) · Food Research International · doi:10.1016/j.foodres.2025.116380 · Cited by 1 · see citing works
Label accuracy of commercial probiotics—CFU enumeration and microbial composition
Čuljak, N., Repić, I., Čanak, I., et al. (2026) · Annals of Microbiology · doi:10.1186/s13213-026-01854-w · Cited by 1 · see citing works
“Although labelling inaccuracies in probiotic products have already been reported (Wang et al. 2026; da Silva et al. 2024; Liang et al. 2024; Syromyatnikov et al. 2022; Ullah et al. 2019; Morovic et al. 2016), no systematic DNA-based evaluation has been performed on products marketed in Croatia.”
Bacterial phenotype prediction based on methylation site profiles
Nykrýnová, M., Bezdíček, M., Lengerová, M., et al. (2023) · IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) · doi:10.1109/cibcb56990.2023.10264900 · Cited by 1 · see citing works
Madhumathi, I., Ramesh, V., Rathakrishnan, B., Abirami, B., Gunasekaran, K., Kumar, T. S., Jeyasankar, P., Raja, G., Selvam, K., Rajendran, S., et al. (2026) · Gut microbes reports · doi:10.1080/29933935.2026.2668863
“24,25 A recurring issue across multiple products was the discrepancy between labeled and actual contents, as revealed by MALDI-TOF-based identification and genomic sequencing.”
A Survey of Commercially Available Probiotics
Misra, S., & Raghuwanshi, S. (2023) · Springer eBooks · doi:10.1007/978-981-99-1463-0_24
Probiotic Identity from Spore: Focus on Bacillus Probiotics
Bhanuramanand, K., Veena, P. V. S., Haritha Rani, B., Mehta, D. S., DeSouza, A., & Nalam, M. R. (2023) · Springer eBooks · doi:10.1007/978-981-99-1463-0_26
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Changes in the Gut Microbiome as Seen in Diabetes and Obesity
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Microbiome-Based Therapeutics for the Management of Cancer
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Dorosky, R. J., Schreier, J. E., Lola, S. L., Sava, R. L., Coryell, M. P., Akue, A. D., KuKuruga, M. A., Carlson, P. E., Dreher‐Lesnick, S. M., & Stibitz, S. (2024) · Figshare · doi:10.6084/m9.figshare.25036279
Microbiological Safety of Probiotic Food Supplements
Ziegler, D., Stark, J., Meier, S., & Brodmann, P. (2026) · Food Risk Assess Europe · doi:10.2903/fr.efsa.2026.fr-0088
Zooming into the microbial and metabolic effects of citicoline use in kefir
Barel, M. (2025) · International Journal of Food Science & Technology · doi:10.1093/ijfood/vvag007
Vikström, S., Lundqvist, C., Säljö, J. F., et al. (2026) · Food and Bioprocess Technology · doi:10.1007/s11947-026-04353-7
“…bacteria after drying processes is a challenge in the industry, and many products actually do not meet the stated content in terms of colony-forming units on the label within the specified shelf life (Drago et al., 2010; Elliot & Teversham, 2004; Morovic et al., 2016; Temmer-man et al., 2003).”
Song, Z., Jiang, Q., Jiao, Y., et al. (2026) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2026.107561
Probiotics for Primary or Secondary Prevention of Clostridioides difficile Infection
Kaiser-Powers, T., & Weingarden, A. R. (2026) · Gastroenterology Clinics of North America · doi:10.1016/j.gtc.2026.05.004
Todhanakasem, T., Sanchan, N., Kaituam, P., & Wu, B. (2026) · Foods · doi:10.3390/foods15152745 · Cited by 1 · see citing works
Factors Affecting the Stability of Probiotics in Pharmaceutical Products: A Comprehensive Review
Begum, K., Afrose, S. D., Setu, M. A., & Shohan, M. H. (2026) · International Journal of Medical Sciences and Pharma Research · doi:10.22270/ijmspr.v12i3.195
Brousilová, T., Vlková, E., Bunešová, V., Musilová, Š., & Modráčková, N. (2026) · Frontiers in Nutrition · doi:10.3389/fnut.2026.1933900
“The lack of a harmonized legal category and standardized analytical oversight has resulted in frequent discrepancies between declared and actual CFU counts at consumption (11–14).”
- Authors
- Morovic, W., Hibberd, A. A., Zabel, B., Barrangou, R., & Stahl, B.
- Affiliations
- DuPont (United States) (US)
- North Carolina State University (US)
- Corresponding author
- Stahl, Buffy
- Venue
- Frontiers in Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2016-11-03
- Volume
- 7
- Pages
- 1747-1747
- ISSN
- 1664-302X (ISSN-L)
- PMC
- PMC5093124
- OpenAlex
- W2548672526
- Semantic Scholar
- 21754eb7fb26fcda0a609608a0bcbf1dbfcc9246
- Cited by
- 99
- References
- 45
- Citations by year
- 2026: 9 · 2025: 6 · 2024: 11 · 2023: 15 · 2022: 10 · 2021: 12 · 2020: 15 · 2019: 11 · 2018: 4 · 2017: 6
- FWCI
- 8.82
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Frontiers in Microbiology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- DuPont
- Topics
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Identification and Quantification in Food
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- probiotics, dietary supplements, commercial probiotic products, 16S rRNA gene sequencing, colony-forming units, Lactobacillus acidophilus, Bifidobacterium animalis subsp. lactis, microbial community composition, microbiome
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