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Lan Z, Zhang X, Xu M, Kong J, Zuo X, Wang Y, Wang C, Teng Y, Ni Y, Zhang Y. Whole-genome resequencing and transcriptional profiling association analysis revealed the intraspecies difference response to oligosaccharides utilization in Bifidobacterium animalis subsp. lactis. Front Microbiol 2024; 15:1375384. [PMID: 38659979 PMCID: PMC11041377 DOI: 10.3389/fmicb.2024.1375384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction As prebiotics, oligosaccharides are frequently combined with Bifidobacterium to develop synbiotic products. However, a highly diverse gene repertoire of Bifidobacterium is involved in sugar catabolism, and even phylogenetically close species may differ in their sugar utilization capabilities. To further explore the mechanism underlying the differences in Bifidobacterium animalis subsp. lactis oligosaccharide metabolism. Methods This study screened strains with differential oligosaccharide metabolism. Subsequently, these strains were subjected to genome-wide resequencing and RT-qPCR. Results The resequencing results indicated that the subspecies of B. animalis subsp. lactis had a high genome similarity. The RT-qPCR results revealed that glycosidase genes exhibited consistency in the phenotype of metabolism at the transcriptional level; the better the growth of the strains on the oligosaccharides, the higher was the expression of glycosidase genes related to the oligosaccharides. Our results suggested that the differences in the gene transcription levels led to intraspecies differences in the ability of the strains to metabolize oligosaccharides even when they belonged to the same subspecies. Discussion Future studies with more sample size could generalizable the conclusion to all B. animalis subsp. lactis strains, thus would lay the theoretical foundation for the utilization of the B. animalis subsp. lactis strain as probiotics and the development of synbiotic products.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi, Xinjiang Province, China
| | - Yan Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, Xinjiang Province, China
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Nogacka AM, Cuesta I, Gueimonde M, de los Reyes-Gavilán CG. 2-Fucosyllactose Metabolism by Bifidobacteria Promotes Lactobacilli Growth in Co-Culture. Microorganisms 2023; 11:2659. [PMID: 38004671 PMCID: PMC10673426 DOI: 10.3390/microorganisms11112659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/26/2023] Open
Abstract
Breastfeeding is recognized as the gold standard in infant nutrition, not only because of breastmilk's intrinsic nutritional benefits but also due to the high content of different bioactive components such as 2-fucosyllactose (2'FL) in the mother's milk. It promotes the growth of its two major consumers, Bifidobacterium longum ssp. infantis and Bifidobacterium bifidum, but the effect on other intestinal microorganisms of infant microbiota remains incompletely understood. pH-uncontrolled fecal cultures from infants donors identified as "fast 2'FL -degrader" microbiota phenotype were used for the isolation of 2'FL-associated microorganisms. The use of specific selective agents allowed the successful isolation of B. bifidum IPLA20048 and of Lactobacillus gasseri IPLA20136. The characterization of 2'FL consumption and its moieties has revealed more pronounced growth, pH drop, and lactic acid production after 2'FL consumption when both microorganisms were grown together. The results point to an association between B. bifidum IPLA20048 and L. gasseri IPLA20136 in which L. gasseri is able to use the galactose from the lactose moiety after the hydrolysis of 2'FL by B. bifidum. The additional screening of two groups of bifidobacteria (n = 38), fast and slow degraders of 2'FL, in co-culture with lactobacilli confirmed a potential cross-feeding mechanism based on degradation products released from bifidobacterial 2'FL break-down. Our work suggests that this phenomenon may be widespread among lactobacilli and bifidobacteria in the infant gut. More investigation is needed to decipher how the ability to degrade 2'FL and other human milk oligosaccharides could influence the microbiota establishment in neonates and the evolution of the microbiota in adult life.
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Affiliation(s)
- Alicja M. Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain
| | - Isabel Cuesta
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain
| | - Clara G. de los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (I.C.); (M.G.); (C.G.d.l.R.-G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain
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Zhang G, Sun H, Xu Z, Tan Z, Xiao L, He M, Shang J, Tsapieva AN, Zhang L. Screening of Bifidobacteria with Probiotic Potential from Healthy Infant Feces by Using 2'-Fucosyllactose. Foods 2023; 12:foods12040858. [PMID: 36832933 PMCID: PMC9957139 DOI: 10.3390/foods12040858] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Using 2'-fucosyllactose (2'-FL) as the sole carbon source can be an efficient way to screen bifidobacteria with superior probiotic capabilities since 2'-FL is a key element in promoting the growth of intestinal bifidobacteria in newborns. This approach was used in this work to screen eight bifidobacteria strains, including one strain of Bifidobacterium longum subsp. infantis BI_Y46 and seven strains of Bifidobacterium bifidum (BB_Y10, BB_Y30, BB_Y39, BB_S40, BB_H4, BB_H5 and BB_H22). Studies on their probiotic properties showed that BI_Y46 had a unique morphology with pilus-like structure, a high resistance to bile salt stimulation and a potent inhibitory action on Escherichia coli ATCC 25922. Similarly, BB_H5 and BB_H22 produced more extracellular polysaccharides and had a higher protein content than other strains. In contrast, BB_Y22 displayed considerable auto-aggregation activity and a high resistance to bile salt stimulation. Interestingly, BB_Y39 with weak self-aggregation ability and acid resistance had very excellent bile salt tolerance, extracellular polysaccharides (EPS) production and bacteriostatic ability. In conclusion, 2'-FL was used as sole carbon source to identify eight bifidobacteria with excellent probiotic properties.
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Affiliation(s)
- Gongsheng Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Hui Sun
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Zihe Xu
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Ze Tan
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lihong Xiao
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Mingxue He
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Jiaqi Shang
- Key Laboratory of Bionic Engineering, Ministry of Education, College of Biological and Agricultural Engineering, Jilin University, Changchun 130022, China
| | - Anna N. Tsapieva
- Department of Molecular Microbiology, FSBSI Institute of Experimental Medicine, Acad. Pavlov Street, 12, 197376 St. Petersburg, Russia
| | - Lili Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science, Northeast Agricultural University, Harbin 150030, China
- Correspondence: ; Tel.: +86-451-5519-0675
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Mao B, He Z, Chen Y, Stanton C, Ross RP, Zhao J, Chen W, Yang B. Effects of Bifidobacterium with the Ability of 2'-Fucosyllactose Utilization on Intestinal Microecology of Mice. Nutrients 2022; 14:nu14245392. [PMID: 36558551 PMCID: PMC9785880 DOI: 10.3390/nu14245392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
In breast milk, 2'-Fucosyllactose (2'FL) is the most abundant breast milk oligosaccharide and can selectively promote the proliferation of bifidobacteria. This study aimed to explore the effect of ifidobacterial with different utilization capacities of 2'FL on the intestinal microecology of mice. Furthermore, the effects of ifidobacterial with different 2'FL utilization capabilities on mice gut microbiota under the competitive pressure of 2'FL as a carbon source were explored. Compared with the control group, 2'FL, Bifidobacterium (B.) bifidum M130R01M51 + 2'FL, B. longum subsp. Longum CCFM752, and CCFM752 + 2'FL treatments significantly decreased the food intake. Moreover, the water intake, body weight, and fecal water content in all groups showed no significant difference compared with the control group. The combination of B. longum subsp. longum CCFM752 and 2'FL can significantly increase the levels of pro-inflammatory and anti-inflammatory factors. B. bifidum M130R01M51 and mixed strains combined with 2'FL significantly increased the contents of acetic acid and isobutyric acid. The results showed that B. bifidum M130R01M51, B. breve FHuNCS6M1, B. longum subsp. longum CCFM752, and B. longum subsp. infantis SDZC2M4 combined with 2'FL significantly increased the species richness of the gut microbiota. Moreover, B. longum subsp. longum CCFM752 and B. longum subsp. infantis SDZC2M4 significantly increased the abundance of Faecalibaculum and Bifidobacterium, respectively. In conclusion, exploring the impact on intestinal microecology can provide theoretical guidance for the development of personalized prebiotics for different bifidobacteria, which has the potential to improve the ecological imbalance of infant gut microbiota.
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Affiliation(s)
- Bingyong Mao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Zhujun He
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yang Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Catherine Stanton
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China
- APC Microbiome Ireland, University College Cork, T12 R229 Cork, Ireland
- Teagasc Food Research Centre, Moorepark, Co., P61 C996 Cork, Ireland
| | - Reynolds Paul Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China
- APC Microbiome Ireland, University College Cork, T12 R229 Cork, Ireland
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
| | - Bo Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi 214122, China
- Correspondence:
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5
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Ding M, Zheng Y, Liu F, Tian F, Ross RP, Stanton C, Yu R, Zhao J, Zhang H, Yang B, Chen W. Lactation time influences the composition of Bifidobacterium and Lactobacillus at species level in human breast milk. Benef Microbes 2022; 13:319-330. [PMID: 35979712 DOI: 10.3920/bm2021.0119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human breast milk is a source of microorganisms for infants that play an important role in building infant gut health and immunity. The bacterial composition in human breast milk is influenced by lactation time. This study aimed to investigate the influence of lactation time on bacteria in breast milk at the genus level and the species levels of Bifidobacterium and Lactobacillus on days 2-4, 8, 14, and 30. Eighteen individuals were recruited and 60 milk samples were collected. The 16S rRNA gene, and the bifidobacterial groEL and lactobacilli groEL genes were used for amplicon sequencing. The results revealed that the alpha diversities of colostrum and transition 1 (day 8) milk were lower than that of transition 2 (day 14) and mature milk. PCoA analysis showed that bacterial composition in colostrum and transition 1 milk differed from transition 2 and mature milk. A lower relative abundance of Blautia was found in colostrum and transition 1 milk compared with mature milk and lower abundances of Ruminococcus, Dorea, and Escherichia-Shigella were found in transition 1 compared with mature milk. Bifidobacterium ruminantium, Limosilactobacillus mucosae, and Ligilactobacillus ruminis were the predominant species across all four lactation stages, while Bifidobacterium bifidum was lower in transition 1, and Bifidobacterium pseudocatenulatum and Bifidobacterium pseudolongum were higher in transition 1 milk. This study indicated that the bacterial composition in colostrum was more similar to that of transition 1 milk, whereas the bacterial community in transition 2 milk was similar to that of mature milk which suggests that bacterial composition in human breast milk shows stage-specific signatures even within a short period at both genus level and Bifidobacterium and Lactobacillus species levels, providing insights into probiotic supplementation for the nursing mother.
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Affiliation(s)
- M Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China P.R.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122 Jiangsu, China P.R
| | - Y Zheng
- H&H Global Research and Technology Center, Guangzhou, China P.R
| | - F Liu
- H&H Global Research and Technology Center, Guangzhou, China P.R
| | - F Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China P.R.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122 Jiangsu, China P.R
| | - R P Ross
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China P.R.,APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - C Stanton
- International Joint Research Center for Probiotics & Gut Health, Jiangnan University, Wuxi, Jiangsu, China P.R.,APC Microbiome Ireland, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Cork P61 C996, Ireland
| | - R Yu
- Department of Neonatology, The Affiliated Wuxi Maternity and Child Health Care Hospital of Nanjing Medical University,48 Huaishu Alley, Liangxi District, Wuxi, 214002, China P.R
| | - J Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China P.R.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122 Jiangsu, China P.R
| | - H Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China P.R.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122 Jiangsu, China P.R.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China P.R.,Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi, China P.R
| | - B Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China P.R.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122 Jiangsu, China P.R.,H&H Global Research and Technology Center, Guangzhou, China P.R
| | - W Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China P.R.,School of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122 Jiangsu, China P.R.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu, China P.R
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6
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Nogacka AM, Arboleya S, Nikpoor N, Auger J, Salazar N, Cuesta I, Alvarez-Buylla JR, Mantecón L, Solís G, Gueimonde M, Tompkins TA, de los Reyes-Gavilán CG. In Vitro Probiotic Modulation of the Intestinal Microbiota and 2′Fucosyllactose Consumption in Fecal Cultures from Infants at Two Months of Age. Microorganisms 2022; 10:microorganisms10020318. [PMID: 35208773 PMCID: PMC8876326 DOI: 10.3390/microorganisms10020318] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/26/2022] [Accepted: 01/26/2022] [Indexed: 01/17/2023] Open
Abstract
2′-fucosyllactose (2′FL) is one of the most abundant oligosaccharides in human milk, with benefits on neonatal health. Previous results point to the inability of the fecal microbiota from some infants to ferment 2′FL. We evaluated a probiotic formulation, including the strains Lactobacillus helveticus Rosell®-52 (R0052), Bifidobacterium longum subsp. infantis Rosell®-33 (R0033), and Bifidobacterium bifidum Rosell®-71 (R0071), individually or in an 80:10:10 combination on the microbiota and 2′FL degradation. Independent batch fermentations were performed with feces from six full-term infant donors of two months of age (three breastfed and three formula-fed) with added probiotic formulation or the constituent strains in the presence of 2′FL. Microbiota composition was analyzed by 16S rRNA gene sequencing. Gas accumulation, pH decrease and 2′FL consumption, and levels of different metabolites were determined by chromatography. B. bifidum R0071 was the sole microorganism promoting a partial increase of 2′FL degradation during fermentation in fecal cultures of 2′FL slow-degrading donors. However, major changes in microbiota composition and metabolic activity occurred with L. helveticus R0052 or the probiotic formulation in cultures of slow degraders. Further studies are needed to decipher the role of the host intestinal microbiota in the efficacy of these strains.
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Affiliation(s)
- Alicja M. Nogacka
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (S.A.); (N.S.); (I.C.); (J.R.A.-B.); (M.G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain; (L.M.); (G.S.)
- Correspondence: (A.M.N.); (C.G.d.l.R.-G.); Tel.: +34-985-89-21-31 (A.M.N.)
| | - Silvia Arboleya
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (S.A.); (N.S.); (I.C.); (J.R.A.-B.); (M.G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain; (L.M.); (G.S.)
| | - Naghmeh Nikpoor
- Rosell Institute for Microbiome and Probiotics, Montreal, QC H4P 2R2, Canada; (N.N.); (J.A.); (T.A.T.)
| | - Jeremie Auger
- Rosell Institute for Microbiome and Probiotics, Montreal, QC H4P 2R2, Canada; (N.N.); (J.A.); (T.A.T.)
| | - Nuria Salazar
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (S.A.); (N.S.); (I.C.); (J.R.A.-B.); (M.G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain; (L.M.); (G.S.)
| | - Isabel Cuesta
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (S.A.); (N.S.); (I.C.); (J.R.A.-B.); (M.G.)
| | - Jorge R. Alvarez-Buylla
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (S.A.); (N.S.); (I.C.); (J.R.A.-B.); (M.G.)
| | - Laura Mantecón
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain; (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Asturias, Spain
| | - Gonzalo Solís
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain; (L.M.); (G.S.)
- Pediatrics Service, Central University Hospital of Asturias (HUCA-SESPA), 33011 Oviedo, Asturias, Spain
| | - Miguel Gueimonde
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (S.A.); (N.S.); (I.C.); (J.R.A.-B.); (M.G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain; (L.M.); (G.S.)
| | - Thomas A. Tompkins
- Rosell Institute for Microbiome and Probiotics, Montreal, QC H4P 2R2, Canada; (N.N.); (J.A.); (T.A.T.)
| | - Clara G. de los Reyes-Gavilán
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain; (S.A.); (N.S.); (I.C.); (J.R.A.-B.); (M.G.)
- Institute of Health Research of the Principality of Asturias (ISPA), 33011 Oviedo, Asturias, Spain; (L.M.); (G.S.)
- Correspondence: (A.M.N.); (C.G.d.l.R.-G.); Tel.: +34-985-89-21-31 (A.M.N.)
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7
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Díaz R, Torres-Miranda A, Orellana G, Garrido D. Comparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota. Microorganisms 2021; 9:microorganisms9091906. [PMID: 34576801 PMCID: PMC8470182 DOI: 10.3390/microorganisms9091906] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/03/2022] Open
Abstract
Bifidobacterium longum subsp. longum is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional diversity. In this study, 154 genomes from public databases and four new Chilean isolates were genomically compared through an in silico approach to identify genomic divergence in genes associated with carbohydrate consumption and their possible adaptations to different human intestinal niches. The pangenome of the subspecies was open, which correlates with its remarkable ability to colonize several niches. The new genomes homogenously clustered within subspecies longum, as observed in phylogenetic analysis. B. longum SC664 was different at the sequence level but not in its functions. COG analysis revealed that carbohydrate use is variable among longum subspecies. Glycosyl hydrolases participating in human milk oligosaccharide use were found in certain infant and adult genomes. Predictive genomic analysis revealed that B. longum M12 contained an HMO cluster associated with the use of fucosylated HMOs but only endowed with a GH95, being able to grow in 2-fucosyllactose as the sole carbon source. This study identifies novel genomes with distinct adaptations to HMOs and highlights the plasticity of B. longum subsp. longum to colonize the human gut microbiota.
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