Bifidobacterium longum, a Predominant Bifidobacterium in Early-life Infant Potentially Used as Probiotic

Dyah Fitri Kusharyati, Anwar Rovik, Dini Ryandini, Hendro Pramono


In early life, Bifidobacteria are reported as dominant bacteria in the human digestive tract. Bifidobacterium is potential as a probiotic. The probiotic property of Bifidobacterium is strain-specific. This study aimed to identify the Bifidobacterium (isolated from less than one-month-old healthy infant stool that potentially used as probiotic) based on the 16S rRNA gene and determining their similarities among Bifidobacteria. The probiotic-potentially Bifidobacterium was re-characterized by performing a Gram’s staining and catalase test. The DNA extraction process was followed by the 16S rRNA amplification using 27F-1492R primers. Sequence similarity was checked by using the BLAST program in the GenBank. The phylogenetic tree was constructed by using a neighbor-joining (NJ) method within the MEGA version 7.0 package. The 16S rRNA gene was presented at 1,500 bp length. Bifidobacterium strains have a 91.14-94.26 % sequence similarity to B. longum subsp. longum strain CCUG30698 which is considered as insufficient for species and genus identifications. However, those isolates could be assigned in a phylogenetic position. This present study suggested the B. longum as the dominant strain of Bifidobacterium in the gut of early-life infants which has potential as a probiotic and is considered as an ideal probiotic for human consumption. This study is useful as basic information for other related research, as well as its application in industrial or community service fields.


16S rRNA; Bifidobacterium longum; Infant Stool; Probiotic


Aloisio, I., Santini, C., Biavati, B., Dinelli, G., Cencič, A., & Chingwaru, W. (2012). Characterization of Bifidobacterium spp. strains for the treatment of enteric disorders in newborns. Applied Microbiology and Biotechnology, 96, 1561–1576.

Attri, S., Mahajan, R., & Goel, G. (2018). Development and diversity of lactic acid-producing bacteria and bifidobacteria in healthy full-term Indian infants from Himachal Pradesh. Intestine Research, 16(4), 529-536.

Benga, L., Peter, W., Benten, M., Engelhardt, E., Kohrer, K., Gougoula, C., & Sager, M. (2014). 16S ribosomal DNA sequence-based identification of bacteria in laboratory rodents: a practical approach in laboratory animal bacteriology diagnostics. Laboratory Animals, 48(4), 305-312.

Chaplin, A.V., Efimov, B.A., Smeianov, V.V., Kafarskaia, L.I., Pikina, A.P., & Shkoporov, A.N. (2015). Intraspecies genomic diversity and long-term persistence of Bifidobacterium longum. PLoS One, 10(8), e0135658.

Da-Silva, M.A.C., Cavalett, A., Spinner, A., Rosa, D.C., Jasper, R.B., Quecine, M.C., Bonatelli, M.L., Kleiner, A.P., Corção, G, & Lima, A.O.S. (2013). Phylogenetic identification of marine bacteria isolated from deep-sea sediments of the Eastern South Atlantic Ocean. Springer Plus, (2), 127.

Devaraj, S., Hemarajata, P., & Versalovic, J. (2013). The human gut microbiome and body metabolism: implications for obesity and diabetes. Clinical Chemistry, 59, 617-628.

Duranti, S., Lugli, G.A., Mancabelli, L., Armanini, F., Turroni, F., James, K., Ferreti, P., Gorfer, V., Ferrario, C., Milani, C., Mangifesta, M., Anzalone, R., Zolfo, M., Viappiani, A., Pasolli, E., Bariletti, I., Canto, R., Clementi, R., Cologna, M., Crifo, T., Cusumano, G., Fedi, S., Gottardi, S., Innamorati, C., Mase, C., Postai, D., Savio, D., Soffiati, M., Tateo, S., Pedrotti, A., Segata, N., Van-Sinderen, D., & Ventura, M. (2017). Maternal inheritance of bifidobacterial communities and bifidophages in infants through vertical transmission. Microbiome, 5(66).

Eshaghia, M., Bibalana, M.H., Rohanibe, M., Esghaeic, M., Masoumeh, Malihe, D., Mohammad, T., & Pourshafie, R. (2017). Bifidobacterium obtained from mother's milk and their infant stool: a comparative genotyping and antibacterial analysis. Microbial Pathogenesis, 111, 94-98.

Gouba, N., Hien, Y.E., Guissou, M.L., Fonkou, M.D.M., Traore, Y., & Tarnagda, Z. (2019). Digestive tract mycobiota and microbiota and the effects on the immune system. Human Microbiome Journal, 12, 1000056.

Kasi, P.D., Ariandi, & Tenriawaru, E.P. (2019). Identifikasi bakteri asam laktat dari limbah cair sagu dengan gen 16S rRNA. Majalah Ilmiah Biologi Biosfera, 36(1), 35-40.

Kolondam, B.J. (2020). Evaluasi deteksi berbasis PCR untuk bakteri Bifidobacterium longum dalam sampel feses bayi dari Kota Manado. Jurnal Ilmiah Sains, 20(1), 18-25.

Kusharyati, D.F., Pramono, H., Ryandini, D., Manshur, T.A., Dewi, M.A., Khatimah, K., & Rovik, A. (2020). Bifidobacterium from infant stool: the diversity and potential screening. Biodiversitas, 21(6), 2506-2513.

Lawson, M.A.E., O'Neill, I.J., Kujawska, M., Javvadi, S.G., Wijeyesekara, A., Flegg, Z., Chalklen, L., & Hall, L.J. (2020). Breast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem. ISME Journal, 14, 635-648.

Liu, W.J., Chen, Y.F., Kwok, L.Y., Li, M.H., Sun, T., Sun, C.L., Wang, X.N., Dan, T., Menghebilige, Zhang, H.P., & Sun, T.S. (2013). Preliminary selection for potential probiotic bifidobacterium isolated from subjects of different Chinese ethnic groups and evaluation of their fermentation and storage characteristics in bovine milk. Journal of Dairy Science, 96, 6807-6817.

Lomasney, K.W., Cryan, J.F., & Hyland, N.P. (2014). Converging effects of a Bifidobacterium and Lactobacillus probiotic strain on mouse intestinal physiology. American Journal of Gastrointestine and Liver Physiology, 307, G241–G247.

Makino, H. (2018). Bifidobacteria strains in the intestines of newborns originate from their mothers. Bioscience of Microbiota, Food and Health, 37(4), 79-85.

Malviya, N., Yadav, A.K., Yandigeri, M.S., & Arora, D.K. (2011). Diversity of culturable streptomycetes from wheat cropping system of fertile regions of Indo-Gangetic Plains, India. World Journal of Microbiology and Biotechnology, 27, 1593-1602.

Mariat, D., Firmesse, O., Levenez, F., Guimaraes, V.D., Sokol, H., & Dore, J. (2019). The Firmicutes/Bacteroides ratio of the human microbiota changes with age. BioMed Central Microbiology, 9, 123.

Martin, R., Makino, H., Yavuz, A., Ben-Amor, K., Roelofs, M., Ishikawa, E., Kubota, H., Swinkels, S., Sakai, T., Oishi, K., Kushiro, A., & Knol, J. (2016). Early-life events, including mode of delivery and type of feeding, siblings, and gender, shape the developing gut microbiota. PLoS One, 11, e0158498.

Milani, C., Hevia, A., Foroni, E., Duranti, S., Turroni, F., Lugli, G.A., Sanchez, B., Martin, R., Gueimonde, M., van-Sinderen, D., Margolles, A., & Ventura, M. (2013). Assessing the fecal microbiota: an optimized ion torrent 16S rRNA gene-based analysis protocol. PLoS One, 8(7), e68739.

Morita, H., Nakano, A., Onoda, H., Toh, H., Oshima, K., Takami, H., Murakami, M., Fukuda, S., Takizawa, T., Kuwahara, T., Ohno, H., Tanabe, S., & Hattori, M. (2011). Bifidobacterium kashiwanohense sp. nov., isolated from healthy infant feces. International Journal of Systematic and Evolutionary Microbiology, 61, 2610-2615.

Murphy, K., Curley, D., O’Callaghan, T.F., O’Shea C-A., Dempsey, E.M., O’Toole, P.W., Ross, R.P., Ryan, A., & Stanton, C. (2017). The composition of human milk and infant fecal microbiota over the first three months of life: a pilot study. Scientific Reports, 7, 40597.

Nagpal, R., Mainali, R., Ahmadi, S., Wang, S., Singh, R., Kavanagh, K., & Yadav, H. (2018). Gut microbiome and aging: physiological and mechanistic insights. Nutrition and Healthy Aging, 4(4), 267-285.

Narayanan, R. & Subramonian, B.S. (2015). Effect of prebiotics on bifidobacterial species isolated from infant feces. Indian Journal of Traditional Knowledge, 14(2), 285-289.

Oishi, K., Martin, R., Ben-Amor, K., Knol, J., & Tanaka, R. (2013). Mother-to-infant transmission of intestinal Bifidobacteria strains has an impact on the early development of vaginally delivered infant's microbiota. PLoS One, 8(11), e78331.

Oki, K., Akiyama, T., Matsuda, K., Gawad, A., Makino, H., Ishikawa, E., Oishi, K., Kushiro, A., & Fujimoto, J. (2018). Long-term colonization exceeding six years from early infancy of Bifidobacterium longum subsp. longum in the human gut. BioMed Central Microbiology, 18(209), 1-13.

Pacheco, A.R., Barile, D., Underwood, M.A., & Mills, D.A. (2015). The impact of milk glycobiome on the neonate gut microbiota. Annual Review of Animal Bioscience, 16(3), 419-445.

Roger, L.C., Costabile, A., Holland, D.T., Hoyles, L., & McCartney, A.L. (2010). Examination of fecal Bifidobacterium populations in breast- and formula-fed infants during the first 18 months of life. Microbiology, 156, 3329-3341.

Russell, D.A., Ross, R.P., Fitzgerald, G.F., & Stanton, C. (2012). Metabolic activities and probiotic potential of bifidobacteria. International Journal of Food Microbiology, 149, 88-105.

Ryandini, D., Pramono, H., & Sukanto. (2018). Antibacterial activity of Streptomyces SAE4034 isolated from the Segara Anakan mangrove rhizosphere against antibiotic-resistant bacteria. Biosaintifika, 10(1), 117-124.

Sim, K., Cox, M.J., Wopereis, H., Martin, R., Knol, J., Li, M.-S., Cookson, W.O., Moffatt, M.F., & Kroll, J.S. (2012). Improved detection of bifidobacteria with optimized 16S rRNA-gene based pyrosequencing. PLoS One, 7, e32543.

Sirilun, S., Takahashi, H., Boonyaritichaikji, S., Chaiyasuti, C., Lertruangpanya, P., Koga, Y., & Mikami, K. (2015). Impact of maternal bifidobacteria and the mode of delivery on bifidobacterium microbiota in infants. Beneficial Microbes, 6(6), 767-774.

Sornplang, P. & Piyadeatsoontorn, S. (2016). Probiotic isolates from unconventional sources: a review. Journal of Animal Science and Technology, 58, 26-37.

Sugahara, H., Odamaki, T., Fukuda, S., Kato, T., Xiao, J.-Z., Abe, F., Kikuchi, J., & Ohno, H. (2015). Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community. Scientific Reports, 5, 13548.

Sun, Z., Zhang, W., Guo, C., Yang, X., Liu, W., & Wu, Y. (2015). Comparative genomic analysis of 45 type strains of the genus Bifidobacterium: a snapshot of its genetic diversity and evolution. PLoS One, 10(2), e0117912.

Walker, A.W., Martin, J.C., Scott, P., Parkhill, J., Flint, H.J., & Scott, K.P. (2015). 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice. Microbiome, 1-11.

Wong, F.W. & Santiago, M. (2017). Microbial approaches for targeting antibiotic-resistant bacteria. Microbial Biotechnology, 10(5), 1047-1053.

Wong, C.B., Odamaki, T., & Xiao, J.-Z. (2019). Beneficial effects of Bifidobacterium longum subsp. longum BB536 on human health: modulation of the gut microbiome as the principal action. Journal of Functional Foods, 54, 506-519.



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