Bifidobacterium aerophilum sp. nov., Bifidobacterium avesanii sp. nov. and Bifidobacterium ramosum sp. nov.: Three novel taxa from the faeces of cotton-top tamarin (Saguinus oedipus L.)
Abstract
Forty-five microorganisms were isolated on bifidobacteria selective medium from one faecal sample of an adult subject of the cotton-top tamarin (Saguinus oedipus L.). All isolates were Gram-positive, catalase-negative, anaerobic, fructose-6-phosphate phosphoketolase positive, and asporogenous rod-shaped bacteria. In this study, only eight out of the forty-five strains were characterized more deeply, whereas the others are still currently under investigation. They were grouped by BOX-PCR into three clusters: Cluster I (TRE 17(T), TRE 7, TRE 26, TRE 32, TRE 33, TRE I), Cluster II (TRE C(T)), and Cluster III (TRE M(T)). Comparative analysis of 16S rRNA gene sequences confirmed the results from the cluster analysis and revealed relatively low level similarities to each other (mean value 95%) and to members of the genus Bifidobacterium. All eight isolates showed the highest level of 16S rRNA gene sequence similarities with Bifidobacterium scardovii DSM 13734(T) (mean value 96.6%). Multilocus sequence analysis (MLSA) of five housekeeping genes (hsp60, rpoB, clpC, dnaJ and dnaG) supported their independent phylogenetic position to each other and to related species of Bifidobacterium. The G+C contents were 63.2%, 65.9% and 63.0% for Cluster I, Cluster II and Cluster III, respectively. Peptidoglycan types were A3α l-Lys-l-Thr-l-Ala, A4β l-Orn (Lys)-d-Ser-d-Glu and A3β l-Orn-l-Ser-l-Ala in Clusters I, II and III, respectively. Based on the data provided, each cluster represented a novel taxon for which the names Bifidobacterium aerophilum sp. nov. (TRE 17(T)=DSM 100689=JCM 30941; TRE 26=DSM 100690=JCM 30942), Bifidobacterium avesanii sp. nov. (TRE C(T)=DSM 100685=JCM 30943) and Bifidobacterium ramosum sp. nov. (TRE M=DSM 100688=JCM 30944) are proposed.
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The phylogenetically related B. bifidum species (PBS) are predominantly inhabitants of the non-human primates' gut.
“The phylogenetically related B. bifidum species (PBS), collectively forming the B. bifidum group, and Ninclude B. aerophilum, B. amazonense, B. biavatii, B. goeldii, B. hapali, B. jacchi, B. leontopitheci, B. miconis, B. ramosum, B. samirii, B. scardovii, and B. simiiventris , are predominantly inhabitants of the non-human primates' gut [25-28] .”
From Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum (2026) · cites this paper as [28]
Cites
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou, N., & Nei, M. (1987) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040454 · Cited by 59,962 · see citing works
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
Felsenstein, J. (1985) · Evolution · doi:10.1111/j.1558-5646.1985.tb00420.x · Cited by 44,735 · see citing works
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013) · Molecular biology and evolution · doi:10.1093/molbev/mst197 · Cited by 41,174 · see citing works
Kimura, M. (1980) · Journal of Molecular Evolution · doi:10.1007/bf01731581 · Cited by 29,778 · see citing works
Bergey's Manual of Systematic Bacteriology
(1990) · Annals of Internal Medicine · doi:10.7326/0003-4819-112-5-391_3 · Cited by 15,633 · see citing works
Talavera, G., & Castresana, J. (2007) · Systematic Biology · doi:10.1080/10635150701472164 · Cited by 5,599 · see citing works
MESBAH, M., PREMACHANDRAN, U., & Whitman, W. B. (1989) · International Journal of Systematic Bacteriology · doi:10.1099/00207713-39-2-159 · Cited by 4,534 · see citing works
Evolution of mammals and their gut microbes
Ley, R. E., Hamady, M., Lozupone, C., Turnbaugh, P. J., Ramey, R. R., Bircher, J. S., Schlegel, M. L., Tucker, T. A., Schrenzel, M. D., Knight, R., et al. (2008) · Science · doi:10.1126/science.1155725 · Cited by 3,747 · see citing works
Determination of DNA base composition by reversed-phase high-performance liquid chromatography
Támaoka, J., & Komagata, K. (1984) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1984.tb01388.x · Cited by 2,420 · see citing works
PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES
Cavalli-Sforza, L. L., & Edwards, A. W. F. (1967) · Evolution · doi:10.1111/j.1558-5646.1967.tb03411.x · Cited by 2,243 · see citing works
A rapid method for the base ratio determination of bacterial DNA
Cashion, P., Holder-Franklin, M. A., McCully, J., & Franklin, M. (1977) · Analytical Biochemistry · doi:10.1016/0003-2697(77)90720-5 · Cited by 1,013 · see citing works
Bergey’s Manual of Systematic Bacteriology
Wade, W. E., & Dewhirst, F. E. (2012) · Springer US · Cited by 649 · see citing works
Schümann, P. (2011) · Methods in microbiology · doi:10.1016/b978-0-12-387730-7.00005-x · Cited by 531 · see citing works
Evolutionary Relationships of Wild Hominids Recapitulated by Gut Microbial Communities
Ochman, H., Worobey, M., Kuo, C., Ndjango, J.-B. N., Peeters, M., Hahn, B. H., & Hugenholtz, P. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000546 · Cited by 498 · see citing works
Martens, M., Dawyndt, P., Coopman, R., et al. (2008) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.65392-0 · Cited by 414 · see citing works
Yıldırım, S., Yeoman, C. J., Sipos, M., Torralba, M., Wilson, B. A., Goldberg, T. L., Stumpf, R. M., Leigh, S. R., White, B. A., & Nelson, K. E. (2010) · PLoS ONE · doi:10.1371/journal.pone.0013963 · Cited by 277 · see citing works
Probiotic Bacteria: Legislative Framework—Requirements to Evidence Basis1,
Piñeiro, M., & Stanton, C. (2007) · Journal of Nutrition · doi:10.1093/jn/137.3.850s · Cited by 261 · see citing works
Lactic Acid Bacteria: Biodiversity and Taxonomy
(2014) · doi:10.1002/9781118655252 · Cited by 225 · see citing works
Insights into the taxonomy, genetics and physiology of bifidobacteria
Ventura, M., van Sinderen, D., Fitzgerald, G. F., & Zink, R. (2004) · Antonie van Leeuwenhoek · doi:10.1023/b:anto.0000047930.11029.ec · Cited by 190 · see citing works
Analysis of bifidobacterial evolution using a multilocus approach
Ventura, M., Canchaya, C. A., Casale, A. D., Dellaglio, F., Neviani, E., Fitzgerald, G. F., & van Sinderen, D. (2006) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.64233-0 · Cited by 158 · see citing works
Jian, W., Zhu, L., & Dong, X. (2001) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/00207713-51-5-1633 · Cited by 140 · see citing works
Modification of the phosphoketolase assay for rapid identification of bifidobacteria
Orban, J. I., & Patterson, J. A. (2000) · Journal of Microbiological Methods · doi:10.1016/s0167-7012(00)00133-0 · Cited by 128 · see citing works
Identification of Bifidobacterium Species Using rep-PCR Fingerprinting
Masco, L., Huys, G. R. B., Gevers, D., Verbrugghen, L., & Swings, J. (2003) · Systematic and Applied Microbiology · doi:10.1078/072320203770865864 · Cited by 110 · see citing works
Mattarelli, P., Holzapfel, W. H., Franz, C. M. A. P., Endo, A., Felis, G. E., Hammes, W. P., Pot, B., Dicks, L. M. T., & Dellaglio, F. (2014) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.060046-0 · Cited by 104 · see citing works
Self-citationTaylor, A. B., & Vinyard, C. J. (2004) · Journal of Morphology · doi:10.1002/jmor.10249 · Cited by 103 · see citing works
Patterns of Gut Bacterial Colonization in Three Primate Species
McKenney, E. A., Rodrigo, A. G., & Yoder, A. D. (2015) · PLoS ONE · doi:10.1371/journal.pone.0124618 · Cited by 81 · see citing works
Bifidobacterium bombi sp. nov., from the bumblebee digestive tract
Killer, J., Kopečný, J., Mrázek, J., et al. (2009) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.002915-0 · Cited by 81 · see citing works
Killer, J., Kopečný, J., Mrázek, J., Koppova, I., Havlík, J., Benada, O., & Kott, T. (2010) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.022525-0 · Cited by 79 · see citing works
Killer, J., Kopečný, J., Mrázek, J., et al. (2010) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2010.08.002 · Cited by 75 · see citing works
Phylogenetic analysis of the fecal flora of the wild pygmy loris
Bo, X., Zun‐xi, H., Wang, X., et al. (2010) · American Journal of Primatology · doi:10.1002/ajp.20826 · Cited by 72 · see citing works
Endo, A., Futagawa-Endo, Y., Schümann, P., et al. (2012) · Systematic and Applied Microbiology · doi:10.1016/j.syapm.2011.11.006 · Cited by 53 · see citing works
Kim, B. J., Kim, H.-Y., Yun, Y.-J., Kim, B., & Kook, Y. (2010) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.020339-0 · Cited by 42 · see citing works
BIAVATI, B., & MATTARELLI, P. (2012) · Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) · Cited by 41 · see citing works
Self-citationBifidobacterium commune sp. nov. isolated from the bumble bee gut
Praet, J., Meeus, I., Cnockaert, M. C., Aerts, M., Smagghe, G. J., & Vandamme, P. A. R. (2015) · Antonie van Leeuwenhoek · doi:10.1007/s10482-015-0425-3 · Cited by 39 · see citing works
Seed Swallowing in Tamarins: Evidence of a Curative Function or Enhanced Foraging Efficiency?
Garber, P. A., & Kitron, U. (1997) · International Journal of Primatology · doi:10.1023/a:1026359105653 · Cited by 35 · see citing works
Tsuchida, S., Takahashi, S., Nguema, P. P. M., et al. (2013) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.055186-0 · Cited by 31 · see citing works
Modesto, M., Michelini, S., Stefanini, I., et al. (2014) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.056937-0 · Cited by 31 · see citing works
Self-citationMichelini, S., Oki, K., Yanokura, E., et al. (2015) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.000708 · Cited by 31 · see citing works
Self-citationBifidobacterium lemurum sp. nov., from faeces of the ring-tailed lemur (Lemur catta)
Modesto, M., Michelini, S., Stefanini, I., Sandri, C., Spiezio, C., Pisi, A., Filippini, G., Biavati, B., & Mattarelli, P. (2015) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijs.0.000162 · Cited by 30 · see citing works
Self-citationThe presence of bifidobacteria in social insects, fish and reptiles
Kopečný, J., Mrázek, J., & Killer, J. (2010) · Folia Microbiologica · doi:10.1007/s12223-010-0053-2 · Cited by 28 · see citing works
Michelini, S., Modesto, M., Oki, K., Stenico, V., Stefanini, I., Biavati, B., Watanabe, K., Ferrara, A., & Mattarelli, P. (2015) · Anaerobe · doi:10.1016/j.anaerobe.2015.03.001 · Cited by 23 · see citing works
Self-citationBifidobacterium eulemuris sp. nov., isolated from faeces of black lemurs (Eulemur macaco)
Michelini, S., Modesto, M., Pisi, A., et al. (2016) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.000924 · Cited by 16 · see citing works
Self-citationThe genera Bifidobacterium, Parascardovia and Scardovia
Mattarelli, P., & Biavati, B. (2014) · doi:10.1002/9781118655252.ch29 · Cited by 8 · see citing works
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Evolutionary development and co‐phylogeny of primate‐associated bifidobacteria
Lugli, G. A., Alessandri, G., Milani, C., Mancabelli, L., Ruiz, L., Fontana, F., Borragán, S., González, A., Turroni, F., Ossiprandi, M. C., et al. (2020) · Environmental Microbiology · doi:10.1111/1462-2920.15108 · Cited by 24 · see citing works
Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19
- Authors
- Michelini, S., Modesto, M., Filippini, G., Spiezio, C., Sandri, C., Biavati, B., Pisi, A., & Mattarelli, P.
- Affiliations
- University of Bologna (IT)
- University of Verona (IT)
- University of Malta (MT)
- Corresponding author
- Mattarelli, Paola
- Venue
- Systematic and Applied Microbiology
- Publisher
- Elsevier BV
- Published
- 2016-06
- Volume
- 39
- Issue
- 4
- Pages
- 229-236
- ISSN
- 0723-2020 (ISSN-L)
- OpenAlex
- W2362277681
- Cited by
- 35
- References
- 44
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 2 · 2022: 1 · 2021: 2 · 2020: 9 · 2019: 6 · 2018: 5 · 2017: 7
- FWCI
- 4.68
- Type
- journal article
- Language
- en
- Update notices
- erratum (2018-09-01)
- Open access
- closed
- Locations
- Systematic and Applied Microbiology (publishedVersion)
- PubMed (publishedVersion)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Medicine › Infectious Diseases › Clostridium difficile and Clostridium perfringens research
- Keywords
- novel bacterial species, cotton-top tamarin, Saguinus oedipus, fecal microbiota, gut microbiota, multilocus sequence analysis, 16S rRNA phylogeny, peptidoglycan type, GC content, anaerobic bacteria, Bifidobacterium scardovii
- MeSH terms
- Aldehyde-Lyases, Animals, Base Composition, Base Sequence, Bifidobacterium, DNA, Bacterial, Feces, Peptidoglycan, Phylogeny, DNA-Directed RNA Polymerases, RNA, Ribosomal, 16S, Saguinus, Sequence Analysis, DNA, Chaperonin 60, DNA Primase, HSP40 Heat-Shock Proteins, Multilocus Sequence Typing
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