The human gut microbiota is composed of numerous bacteria similar in number to human cells, and each individual has their own gut microbiota status.¹ Research on human gut microbiota has grown exponentially in the past 2 decades and has demonstrated that gut microbiota is crucial for maintaining human health. At the same time, it has also been known that dysbiosis is related to many diseases. However, no gut microbiota-based therapy is available in clinical practice other than fecal microbiota transplantation for Clostridioides difficile infection. Only probiotics have been used for more than 100 years in human life, and some antibiotics are on-hand as a modality to improve gut dysbiosis.

Multiple factors, including delivery mode, breastfeeding, diet, medication, exercise, aging, stress, and infection, can influence the gut microbiota.² The widespread inter-individual heterogeneity of gut microbiota composition makes gut microbiota research inconsistent.³ Similarly, when probiotics, living microorganisms by definition, are administered and act on the gut, they can be affected by various factors and each individual’s gut microbiota. In this issue of the Journal of Neurogastroenterology and Motility, Tremblay et al⁴ demonstrated the relationship between the persistence of probiotics and human gut transit time using delicate research methods. When a multi-strain probiotic consisting of 2 Lactobacilli, 2 Bifidobacteria, and 1 Streptococcus was administered to healthy volunteers, Bifidobacterium longum R0175 lasted for more than 15 days, whereas the other strains lasted only 3-6 days after cessation of intake. The longer persistence of B. longum R0175 was observed only in subjects with an intermediate whole gut transit time, and these subjects were confirmed to have a unique gut microbiota composition. It means that the complex relationship between probiotic strain and host-specific factors such as gut transit time and gut microbiota composition determines the persistence of ingested probiotics.

This study suggests several implications for clinicians and researchers using probiotics. The first is the difficulty in clinical research conducted using a probiotic. The results of previously reported clinical trials with probiotics are heterogeneous, even in the same disease, such as irritable bowel syndrome.⁵ The claimed effects of probiotics have recently been questioned owing to the low quality of previous clinical trials by current stringent methodological standards. The low concordance between clinical studies using probiotics was mainly due to their characteristics. To date, a wide variety of strains have been used, individually or in combination. Even for the same strain, the dosage and formulation varied among products. In addition, natural reduction occurs because probiotics are live organisms; therefore, the input amount during manufacturing and the actual number taken are different. These characteristics distinguish probiotics from conventional drugs. To avoid these problems in probiotic clinical trials, experts recommend selecting an appropriate research design in advance by considering the confounding factors above.⁶ Although a parallel design is considered gold standards, a crossover design may reveal more accurate results if underlying gut microbiota is the main determining factor for the effectiveness of probiotics.^6,7 However, the crossover design is discouraged for the unknown carry-over effect of probiotics.⁶ For this issue, Tremblay’s study⁴ provided valuable insights that determining the optimal washout period for each study by considering both probiotic strain and the host-specific parameters is ideal, rather than having a 2-5-week washout period without rationale.

The second is the limitation of the effective use of probiotics in a clinical setting (Figure). Because the effects of probiotics are strain-specific, it is important to select the most effective strain and administer an appropriate dose. In addition to these probiotic factors, inter-individual heterogeneous human gut microbiota may be the main determinant of the effectiveness of probiotic therapy. A recent study showed that the human gut could be permissive or non-permissive to administered probiotics.⁸ This individualized response correlated with baseline host transcriptional and microbiome characteristics. In Tremblay’s study,⁴ the longest persistence of a specific probiotic was observed only in the intermediate whole gut transit group. The gut microbiota composition of this group was characterized by an increased abundance of Blautia, Roseburia, Parabacteroides, and Eggerthella and a reduced abundance of Bifidobacterium, Coprococcus, Erysipelotrichaceae, and Ruminococcaceae. Considering that the longest-persisting probiotic strain was Bifidobacterium, it was presumed that the availability of a specific niche occupied by the same commensal strain or related taxa of administered probiotics in the host gut microbiota was important for the persistence of administered probiotics. However, the concept is not entirely novel. Maldonado-Go’mez et al⁹ reported non-persisters and persisters in humans by administering B. longum AH1206. Persister is associated with lower levels of B. longum and underrepresentation of carbohydrate-utilization genes in pretreated gut microbiota, suggesting niche opportunity.⁹ If so, we can raise another question of whether it is sufficient to check the availability of a niche through next-generation sequencing (NGS) with 16S rRNA gene of stool samples before administering probiotics or needed to evaluate physiological factors, such as gut transit time. There is no answer yet, and further research on this topic should be conducted.

Finally, this study raises the discussion of how to accept the results of the current commonly used gut microbiota research method. Considering the definition of live organisms, longer survival is more desirable. In this regard, longer recovery through NGS analysis does not necessarily mean more effective because the NGS method detects both live and dead bacteria. Another problem is the limitations of the quantitative aspects of commonly used gut microbiota research. NGS technique does not measure the absolute number of bacteria but shows relative abundance.¹⁰ Although the relative proportions of specific taxa are similar, the effect of those taxa may be different between hosts if the absolute amount is different. Therefore, the evaluation of gut microbiota function based on stool NGS analysis may not accurately predict the effectiveness of probiotics. In the future, it will be necessary to develop a simpler bedside monitoring technique that can evaluate functions rather than gut microbiota composition.

Currently, a live biotherapeutic product that is completely different from traditional probiotics is being developed as a novel gut microbiota-based therapy. However, the successful development of live biotherapeutic products does not imply the completion of personalized gut microbiota-based therapies. To achieve complete personalized therapy, assessing the status of gut microbiota and physiology in each individual is a prerequisite. In this respect, more studies should be conducted to identify various confounding factors in host physiology.

This work was supported by Wonkwang University 2022 (S.C.C.).

None.

Yong Sung Kim: design and writing; and Suck Chei Choi: design and final approval.