Isolation and Cultivation of Human Gut Microorganisms: A Review

Overview

Journal Microorganisms

Specialty Microbiology

Date 2023 Apr 28

PMID 37110502

Authors

Xuchun Wan

Qianqian Yang

Xiangfeng Wang

Yun Bai

Zhi Liu

Affiliations

Soon will be listed here.

Abstract

Microbial resources from the human gut may find use in various applications, such as empirical research on the microbiome, the development of probiotic products, and bacteriotherapy. Due to the development of "culturomics", the number of pure bacterial cultures obtained from the human gut has significantly increased since 2012. However, there is still a considerable number of human gut microbes to be isolated and cultured. Thus, to improve the efficiency of obtaining microbial resources from the human gut, some constraints of the current methods, such as labor burden, culture condition, and microbial targetability, still need to be optimized. Here, we overview the general knowledge and recent development of culturomics for human gut microorganisms. Furthermore, we discuss the optimization of several parts of culturomics including sample collection, sample processing, isolation, and cultivation, which may improve the current strategies.

Citing Articles

Consequences of Domestication on Gut Microbiome: A Comparative Analysis Between Wild Boars and Domestic Pigs.

Bae D, Moon S, Lee T, Ko Y, Cho Y, Kang H Animals (Basel). 2025; 15(5).

PMID: 40076031 PMC: 11899531. DOI: 10.3390/ani15050747.

Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.

Reuben R, Torres C World J Microbiol Biotechnol. 2025; 41(2):41.

PMID: 39826029 PMC: 11742929. DOI: 10.1007/s11274-024-04242-1.

Diversity of bacteria within the human gut and its contribution to the functional unity of holobionts.

Rosenberg E NPJ Biofilms Microbiomes. 2024; 10(1):134.

PMID: 39580487 PMC: 11585559. DOI: 10.1038/s41522-024-00580-y.

Microfluidics for studying the deep underground biosphere: from applications to fundamentals.

Morais S, Vidal E, Cario A, Marre S, Ranchou-Peyruse A FEMS Microbiol Ecol. 2024; 100(12).

PMID: 39544108 PMC: 11650873. DOI: 10.1093/femsec/fiae151.

Cutting-Edge iPSC-Based Approaches in Studying Host-Microbe Interactions in Neuropsychiatric Disorders.

Mihailovich M, Sokovic Bajic S, Dinic M, dokic J, Zivkovic M, Radojevic D Int J Mol Sci. 2024; 25(18).

PMID: 39337640 PMC: 11432053. DOI: 10.3390/ijms251810156.

References

Jin H, You L, Zhao F, Li S, Ma T, Kwok L . Hybrid, ultra-deep metagenomic sequencing enables genomic and functional characterization of low-abundance species in the human gut microbiome. Gut Microbes. 2022; 14(1):2021790. PMC: 8786330. DOI: 10.1080/19490976.2021.2021790. View

Batani G, Bayer K, Boge J, Hentschel U, Thomas T . Fluorescence in situ hybridization (FISH) and cell sorting of living bacteria. Sci Rep. 2019; 9(1):18618. PMC: 6901588. DOI: 10.1038/s41598-019-55049-2. View

Jeevarathinam A, Guo F, Williams T, Smolen J, Hyde J, McShane M . Enzyme functionalized microgels enable precise regulation of dissolved oxygen and anaerobe culture. Mater Today Bio. 2021; 9:100092. PMC: 7856461. DOI: 10.1016/j.mtbio.2020.100092. View

Holzhausen E, Nikodemova M, Deblois C, Barnet J, Peppard P, Suen G . Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition. Gut Pathog. 2021; 13(1):75. PMC: 8686582. DOI: 10.1186/s13099-021-00470-0. View

Marcos-Fernandez R, Riestra S, Alonso-Arias R, Ruiz L, Sanchez B, Margolles A . Immunomagnetic Capture of Faecalibacterium prausnitzii Selectively Modifies the Fecal Microbiota and Its Immunomodulatory Profile. Microbiol Spectr. 2023; 11(1):e0181722. PMC: 9927134. DOI: 10.1128/spectrum.01817-22. View

Mailhe M, Ricaboni D, Vitton V, Gonzalez J, Bachar D, Dubourg G . Repertoire of the gut microbiota from stomach to colon using culturomics and next-generation sequencing. BMC Microbiol. 2018; 18(1):157. PMC: 6201554. DOI: 10.1186/s12866-018-1304-7. View

Guan H, Pu Y, Liu C, Lou T, Tan S, Kong M . Comparison of Fecal Collection Methods on Variation in Gut Metagenomics and Untargeted Metabolomics. mSphere. 2021; 6(5):e0063621. PMC: 8550109. DOI: 10.1128/mSphere.00636-21. View

Vlkova E, Salmonova H, Bunesova V, Geigerova M, Rada V, Musilova S . A new medium containing mupirocin, acetic acid, and norfloxacin for the selective cultivation of bifidobacteria. Anaerobe. 2015; 34:27-33. DOI: 10.1016/j.anaerobe.2015.04.001. View

Shen M, Olsthoorn R, Zeng Y, Bakkum T, Kros A, Boyle A . Magnetic-Activated Cell Sorting Using Coiled-Coil Peptides: An Alternative Strategy for Isolating Cells with High Efficiency and Specificity. ACS Appl Mater Interfaces. 2021; 13(10):11621-11630. PMC: 7975280. DOI: 10.1021/acsami.0c22185. View

10.

Lagier J, Khelaifia S, Alou M, Ndongo S, Dione N, Hugon P . Culture of previously uncultured members of the human gut microbiota by culturomics. Nat Microbiol. 2016; 1:16203. DOI: 10.1038/nmicrobiol.2016.203. View

11.

Berdy B, Spoering A, Ling L, Epstein S . In situ cultivation of previously uncultivable microorganisms using the ichip. Nat Protoc. 2018; 12(10):2232-2242. DOI: 10.1038/nprot.2017.074. View

12.

Romano K, Dill-McFarland K, Kasahara K, Kerby R, Vivas E, Amador-Noguez D . Fecal Aliquot Straw Technique (FAST) allows for easy and reproducible subsampling: assessing interpersonal variation in trimethylamine-N-oxide (TMAO) accumulation. Microbiome. 2018; 6(1):91. PMC: 5960144. DOI: 10.1186/s40168-018-0458-8. View

13.

Wang Y, Ai Z, Xing X, Fan Y, Zhang Y, Nan B . The ameliorative effect of probiotics on diet-induced lipid metabolism disorders: A review. Crit Rev Food Sci Nutr. 2022; 64(11):3556-3572. DOI: 10.1080/10408398.2022.2132377. View

14.

Afrizal A, Hitch T, Viehof A, Treichel N, Riedel T, Abt B . Anaerobic single-cell dispensing facilitates the cultivation of human gut bacteria. Environ Microbiol. 2022; 24(9):3861-3881. DOI: 10.1111/1462-2920.15935. View

15.

Maruvada P, Leone V, Kaplan L, Chang E . The Human Microbiome and Obesity: Moving beyond Associations. Cell Host Microbe. 2017; 22(5):589-599. DOI: 10.1016/j.chom.2017.10.005. View

16.

Wilson G, Aitchison L . The use of a combined enrichment-filtration technique for the isolation of Campylobacter spp. from clinical samples. Clin Microbiol Infect. 2007; 13(6):643-4. DOI: 10.1111/j.1469-0691.2007.01712.x. View

17.

Lordan C, Thapa D, Ross R, Cotter P . Potential for enriching next-generation health-promoting gut bacteria through prebiotics and other dietary components. Gut Microbes. 2019; 11(1):1-20. PMC: 6973326. DOI: 10.1080/19490976.2019.1613124. View

18.

Lugli G, Milani C, Duranti S, Alessandri G, Turroni F, Mancabelli L . Isolation of novel gut bifidobacteria using a combination of metagenomic and cultivation approaches. Genome Biol. 2019; 20(1):96. PMC: 6524291. DOI: 10.1186/s13059-019-1711-6. View

19.

Sarhan M, Hamza M, Youssef H, Patz S, Becker M, Elsawey H . Culturomics of the plant prokaryotic microbiome and the dawn of plant-based culture media - A review. J Adv Res. 2019; 19:15-27. PMC: 6630032. DOI: 10.1016/j.jare.2019.04.002. View

20.

Goldenberg J, Ma S, Saxton J, Martzen M, Vandvik P, Thorlund K . Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2013; (5):CD006095. DOI: 10.1002/14651858.CD006095.pub3. View