1
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Ennis D, Shmorak S, Jantscher-Krenn E, Yassour M. Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition. Nat Commun 2024; 15:894. [PMID: 38291346 PMCID: PMC10827747 DOI: 10.1038/s41467-024-45209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
Breast milk contains human milk oligosaccharides (HMOs) that cannot be digested by infants, yet nourish their developing gut microbiome. While Bifidobacterium are the best-known utilizers of individual HMOs, a longitudinal study examining the evolving microbial community at high-resolution coupled with mothers' milk HMO composition is lacking. Here, we developed a high-throughput method to quantify Bifidobacterium longum subsp. infantis (BL. infantis), a proficient HMO-utilizer, and applied it to a longitudinal cohort consisting of 21 mother-infant dyads. We observed substantial changes in the infant gut microbiome over the course of several months, while the HMO composition in mothers' milk remained relatively stable. Although Bifidobacterium species significantly influenced sample variation, no specific HMOs correlated with Bifidobacterium species abundance. Surprisingly, we found that BL. infantis colonization began late in the breastfeeding period both in our cohort and in other geographic locations, highlighting the importance of focusing on BL. infantis dynamics in the infant gut.
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Affiliation(s)
- Dena Ennis
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Shimrit Shmorak
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Moran Yassour
- Microbiology & Molecular Genetics Department, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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2
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Modesto M, Ngom-Bru C, Scarafile D, Bruttin A, Pruvost S, Sarker SA, Ahmed T, Sakwinska O, Mattarelli P, Duboux S. Bifidobacterium longum subsp. iuvenis subsp. nov., a novel subspecies isolated from the faeces of weaning infants. Int J Syst Evol Microbiol 2023; 73. [PMID: 37851001 DOI: 10.1099/ijsem.0.006013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023] Open
Abstract
The species
Bifidobacterium longum
currently comprises four subspecies:
B. longum
subsp.
longum
,
B. longum
subsp.
infantis
,
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
. Recently, several studies on
B. longum
suggested the presence of a separate clade containing four strains isolated from infants and one from rhesus macaque. These strains shared a phylogenetic similarity to
B. longum
subsp.
suis
DSM 20210T and
B. longum
subsp.
suillum
JCM1995T [average nucleotide identity (ANI) of 98.1 %) while showed an ANI of 96.5 % with both
B. longum
subsp.
infantis
and
B. longum
subsp.
longum
. The current work describes five novel additional
B. longum
strains isolated from Bangladeshi weaning infants and demonstrates their common phylogenetic origin with those of the previously proposed separated clade. Based on polyphasic taxonomic approach comprising loci multilocus sequence analysis and whole genome multilocus sequence typing, all ten examined strains have been confirmed as a distinct lineage within the species
B. longum
with
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
as closest subspecies. Interestingly, these strains are present in weaning infants and primates as opposed to their closest relatives which have been typically isolated from pig and calves. These strains, similarly to
B. longum
subsp.
infantis
, show a common capacity to metabolize the human milk oligosaccharide 3-fucosyllactose. Moreover, they harbour a riboflavin synthesis operon, which differentiate them from their closest subspecies,
B. longum
subsp.
suis
and
B. longum
subsp.
suillum
. Based on the consistent results from genotypical, ecological and phenotypical analyses, a novel subspecies with the name
Bifidobacterium longum
subsp. iuvenis, with type strain NCC 5000T (=LMG 32752T=CCOS 2034T), is proposed.
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Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Catherine Ngom-Bru
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Anne Bruttin
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Solenn Pruvost
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Shafiqul Alam Sarker
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Tahmeed Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Olga Sakwinska
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 42, 40127 Bologna, Italy
| | - Stéphane Duboux
- Nestlé Research, Société des Produits Nestlé SA, 1000 Lausanne 26, Switzerland
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3
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A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning. Cell 2022; 185:4280-4297.e12. [PMID: 36323316 DOI: 10.1016/j.cell.2022.10.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/17/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis, indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development.
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4
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Zhang Z, Dong Y, Xiang F, Wang Y, Hou Q, Ni H, Cai W, Liu W, Yang S, Guo Z. Analysis of bacterial diversity and genetic evolution of Lacticaseibacillus paracasei isolates in fermentation pit mud. J Appl Microbiol 2022; 133:1821-1831. [PMID: 35802775 DOI: 10.1111/jam.15672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/13/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022]
Abstract
AIMS Since little is known about the genetic diversity of lactic acid bacteria (LAB) isolates from the fermentation pit mud (FPM), we sought to evaluate the bacterial structure, identify the LAB isolates and investigate the genotype and genetic diversity of the LAB isolates. METHODS AND RESULTS Using high-throughput MiSeq sequencing, we identified seven dominant bacterial genera in FPM. Lactobacillus had the highest abundance. We isolated 55 LAB strains. These isolates were all identified as Lacticaseibacillus paracasei. Using an extant multilocus sequence typing (MLST) scheme, isolates were assigned to 18 sequence types (STs) and three clonal complexes. ST1, the largest group, mainly comprised FPM isolates. Niche-specific ST2 to ST18 only contained FPM isolates. Isolates could be divided into four lineages, with most assigned to Lineage 1. Only one FPM isolate was classified as L. paracasei subsp. paracasei. Other isolates could not be classified at the subspecies level using the seven MLST loci. CONCLUSIONS Lactobacilli account for a high proportion of bacteria in pit mud. Based on the traditional culture method, L. paracasei was the dominant species, and these isolates exhibit a high ethanol tolerance, high intraspecific diversity and specific genetic profiles. SIGNIFICANCE AND IMPACT OF THE STUDY The study described the characterization of FPM bacterial diversity, giving an insight into the genetic diversity of L. paracasei strains present in FPM.
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Affiliation(s)
- Zhendong Zhang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Yun Dong
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Fanshu Xiang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Yurong Wang
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Qiangchuan Hou
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
| | - Hui Ni
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China.,School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, People's Republic of China
| | - Wenchao Cai
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China.,School of Food Science, Shihezi University, Shihezi, Xinjiang Autonomous Region, People's Republic of China
| | - Wenhui Liu
- Hubei Guxiangyang Liquor Industry Co., Ltd., Xiangyang, People's Republic of China
| | - Shaoyong Yang
- Hubei Guxiangyang Liquor Industry Co., Ltd., Xiangyang, People's Republic of China
| | - Zhuang Guo
- Hubei Provincial Engineering and Technology Research Center for Food Ingredients, Hubei University of Arts and Science, Xiangyang, People's Republic of China
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5
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Evaluation of Bacterial Diversity and Evolutionary Dynamics of Gut Bifidobacterium longum Isolates Obtained from Older Individuals in Hubei Province, China. Microbiol Spectr 2022; 10:e0144221. [PMID: 35044201 PMCID: PMC8768838 DOI: 10.1128/spectrum.01442-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bifidobacterium longum predominates in the human gut throughout the life span, from birth to old age, and could alter the intestinal microbial population and immune function in the elderly. We investigated the intestinal bacterial diversity in the elderly, and further evaluated the genetic diversity and population structure of B. longum. The results revealed a distinct difference in gut bacterial populations between the elderly from Xiangyang and its neighboring region, Enshi city. A total of 62 bifidobacterial strains were isolated, 30 of which were found to be B. longum. The multilocus sequence typing (MLST) analysis also revealed that 437 B. longum isolates from diverse regions worldwide, including the 30 isolated in this study, could be classified into 341 sequence types (STs). They could be further clustered into 10 clonal complexes and 127 singleton STs, indicating a highly genetic diversity among B. longum isolates. Two putative clone complexes (CCs) containing the isolates from Xiangyang were found to be geographically specific, and a 213-bp recombination fragment was detected. Phylogenetic trees divided these 437 isolates into three lineages, corresponding to the three subspecies of B. longum. It is noteworthy that two isolates from the elderly were identified to be B. longum subsp. suis, while the others were B. longum subsp. longum. Together, our study characterized the intestinal bacterial diversity and evolution of B. longum in the elderly, and it could contribute to further studies on the genotyping and discrimination of B. longum. IMPORTANCEBifidobacterium longum are common inhabitants of the human gut throughout the life span, and have been associated with health-promoting effects, yet little is known about the genotype profile and evolution of these isolates. Our study showed that there was significant difference in gut bacterial community and abundance of B. longum between the elderly from two neighboring cities. Furthermore, the possible geographically specific STs, CCs, and intraspecies recombination fragment were found among the B. longum isolates from elderly.
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6
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Xiao Y, Zhao J, Zhang H, Zhai Q, Chen W. Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species. Microb Genom 2021; 7:000581. [PMID: 34100697 PMCID: PMC8461469 DOI: 10.1099/mgen.0.000581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 04/12/2021] [Indexed: 12/11/2022] Open
Abstract
Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.
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Affiliation(s)
- Yue Xiao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Hao Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- Yangzhou Institute of Food Biotechnology, Jiangnan University, Yangzhou, Jiangsu 225004, PR China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, PR China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- International Joint Research Laboratory for Probiotics at Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, PR China
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7
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Jena R, Choudhury PK, Puniya AK, Tomar SK. Efficacy of BOX-PCR fingerprinting for taxonomic discrimination of bifidobacterial species isolated from diverse sources. 3 Biotech 2021; 11:270. [PMID: 34055563 DOI: 10.1007/s13205-021-02765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 03/29/2021] [Indexed: 10/21/2022] Open
Abstract
The genus Bifidobacterium are extensively used as probiotics in food applications, for their potential role to combat different lifestyle diseases. This has necessitated a great importance for their species, sub-species and even at the strain level characterization. In the present study, attempts have been made to target repetitive DNA element-based BOX-PCR fingerprinting to judge its potential in taxonomic discrimination of Bifidobacterium species. The BOXA1R primer-based repetitive PCR amplified products were analysed for 93 identified bifidobacterial isolates collected from diverse sources of human and animal origin along with 12 DSMZ procured standard reference strains. Dendrograms constructed from the fingerprint patterns of BOX-PCR differentiated all the isolated strains into 10 different groups, grouped with one standard reference isolates and successfully discriminated all isolates up to subspecies level as identified. The BOX-PCR method used in this study effectively resolved the taxonomic status and differentiated all 93 bifidobacterial species isolated from diverse faecal origins of human and animal samples.
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8
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Kim MJ, Shin SW, Kim HB, Kim E, Kim HY. Direct loop-mediated isothermal amplification (LAMP) assay for rapid on-site detection of Bifidobacterium longum subspecies longum, infantis, and suis in probiotic products. Food Chem 2020; 346:128887. [PMID: 33385916 DOI: 10.1016/j.foodchem.2020.128887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/05/2020] [Accepted: 12/10/2020] [Indexed: 10/22/2022]
Abstract
As interest in probiotics increases, the need for accurate description of probiotic compositions present in commercial products is also increasing. Since Bifidobacterium longum used as probiotics is labeled at species or subspecies levels, a detection method for distinguishing B. longum subsp. longum, infantis, and suis is needed. Thus, we designed three LAMP primer sets for B. longum subspecies. Each primer set was specific for the target subspecies. The detection level was 0.2 pg for each target DNA (about 102 CFU/mL). To apply these LAMP assays to on-site detection, a direct DNA extraction method was optimized and combined with LAMP assay. Finally, direct LAMP assays were used to monitor the presence of B. longum subspecies in 16 probiotic products. They could specifically and sensitively detect target subspecies within approximately 45 min. These rapid on-site detection methods are useful for identifying B. longum subspecies in probiotic products.
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Affiliation(s)
- Mi-Ju Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - So Won Shin
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hyeon-Be Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Eiseul Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences & Resources and Department of Food Science & Biotechnology, Kyung Hee University, Yongin 17104, Republic of Korea.
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9
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Kujawska M, La Rosa SL, Roger LC, Pope PB, Hoyles L, McCartney AL, Hall LJ. Succession of Bifidobacterium longum Strains in Response to a Changing Early Life Nutritional Environment Reveals Dietary Substrate Adaptations. iScience 2020; 23:101368. [PMID: 32721872 PMCID: PMC7390879 DOI: 10.1016/j.isci.2020.101368] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/16/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022] Open
Abstract
Diet-microbe interactions play a crucial role in modulation of the early life microbiota and infant health. Bifidobacterium dominates the breast-fed infant gut and may persist in individuals during transition from a milk-based to a more diversified diet. Here, we investigated adaptation of Bifidobacterium longum to the changing nutritional environment. Genomic characterization of 75 strains isolated from nine either exclusively breast- or formula-fed (pre-weaning) infants in their first 18 months revealed subspecies- and strain-specific intra-individual genomic diversity with respect to carbohydrate metabolism, which corresponded to different dietary stages. Complementary phenotypic studies indicated strain-specific differences in utilization of human milk oligosaccharides and plant carbohydrates, whereas proteomic profiling identified gene clusters involved in metabolism of selected carbohydrates. Our results indicate a strong link between infant diet and B. longum diversity and provide additional insights into possible competitive advantage mechanisms of this Bifidobacterium species and its persistence in a single host.
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Affiliation(s)
- Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Sabina Leanti La Rosa
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Aas, Norway
| | - Laure C Roger
- Department of Food & Nutritional Sciences, University of Reading, Reading RG6 6LA, UK
| | - Phillip B Pope
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Aas, Norway; Faculty of Biosciences, Norwegian University of Life Sciences, 1433 Aas, Norway
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG11 8NS, UK
| | - Anne L McCartney
- Department of Food & Nutritional Sciences, University of Reading, Reading RG6 6LA, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK; Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; Chair of Intestinal Microbiome, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany; ZIEL - Institute for Food & Health, Technical University of Munich, 85354 Freising, Germany.
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10
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Dai H, Lu B, Li Z, Huang Z, Cai H, Yu K, Wang D. Multilocus sequence analysis for the taxonomic updating and identification of the genus Proteus and reclassification of Proteus genospecies 5 O'Hara et al. 2000, Proteus cibarius Hyun et al. 2016 as later heterotypic synonyms of Proteus terrae Behrendt et al. 2015. BMC Microbiol 2020; 20:152. [PMID: 32522175 PMCID: PMC7288399 DOI: 10.1186/s12866-020-01844-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background Members of the genus Proteus are mostly opportunistic pathogens that cause a variety of infections in humans. The molecular evolutionary characteristics and genetic relationships among Proteus species have not been elucidated to date. In this study, we developed a multilocus sequence analysis (MLSA) approach based on five housekeeping genes (HKGs) to delineate phylogenetic relationships of species within the genus Proteus. Results Of all 223 Proteus strains collected in the current study, the phylogenetic tree of five concatenated HKGs (dnaJ, mdh, pyrC, recA and rpoD) divided 223 strains into eleven clusters, which were representative of 11 species of Proteus. Meanwhile, the phylogenetic trees of the five individual HKGs also corresponded to that of the concatenated tree, except for recA, which clustered four strains at an independent cluster. The evaluation of inter- and intraspecies distances of HKG concatenation indicated that all interspecies distances were significantly different from intraspecies distances, which revealed that these HKG concatenations can be used as gene markers to distinguish different Proteus species. Further web-based DNA-DNA hybridization estimated by genome of type strains confirmed the validity of the MLSA, and each of eleven clusters was congruent with the most abundant Proteus species. In addition, we used the established MLSA method to identify the randomly collected Proteus and found that P. mirabilis is the most abundant species. However, the second most abundant species is P. terrae but not P. vulgaris. Combined with the genetic, genomic and phenotypic characteristics, these findings indicate that three species, P. terrae, P. cibarius and Proteus genospecies 5, should be regarded as heterotypic synonyms, and the species should be renamed P. terrae, while Proteus genospecies 5 has not been named to date. Conclusions This study suggested that MLSA is a powerful method for the discrimination and classification of Proteus at the species level. The MLSA scheme provides a rapid and inexpensive means of identifying Proteus strains. The identification of Proteus species determined by the MLSA approach plays an important role in the clinical diagnosis and treatment of Proteus infection.
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Affiliation(s)
- Hang Dai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Binghuai Lu
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Zhenpeng Li
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China
| | - Zhenzhou Huang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Hongyan Cai
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Keyi Yu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China.,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China
| | - Duochun Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), State Key Laboratory of Infectious Disease Prevention and Control, Changbai Road 155, Changping, Beijing, 102206, China. .,Center for Human Pathogen Collection, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206, China.
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11
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Huang CH, Chen CC, Liou JS, Lee AY, Blom J, Lin YC, Huang L, Watanabe K. Genome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae. Int J Syst Evol Microbiol 2020; 70:3755-3762. [DOI: 10.1099/ijsem.0.003969] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Taxonomic relationships between
Lactobacillus casei
,
Lactobacillus paracasei
and
Lactobacillus zeae
have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains
L. casei
ATCC 393T and
L. zeae
ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that
L. casei
could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the
L. zeae
strains, and supported an emended the description of the name of
Lactobacillus zeae
(ex Kuznetsov 1956) Dicks et al. 1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Chih-Chieh Chen
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
- General Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, ROC
- Rapid Screening Research Center for Toxicology and Biomedicine, National Sun Yat-sen University, Kaohsiung 80424, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Ai-Yun Lee
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Yu-Chun Lin
- Livestock Research Institute, Council of Agriculture, Executive Yuan, Tainan, Taiwan, ROC
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, 331 Shih-Pin Rd, Hsinchu 30062, Taiwan, ROC
- Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei 10673, Taiwan, ROC
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12
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Blanco G, Ruiz L, Tamés H, Ruas-Madiedo P, Fdez-Riverola F, Sánchez B, Lourenço A, Margolles A. Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective. Microorganisms 2020; 8:E723. [PMID: 32413974 PMCID: PMC7285499 DOI: 10.3390/microorganisms8050723] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/02/2020] [Accepted: 05/11/2020] [Indexed: 12/18/2022] Open
Abstract
Bifidobacteria are among the most abundant microorganisms inhabiting the intestine of humans and many animals. Within the genus Bifidobacterium, several beneficial effects have been attributed to strains belonging to the subspecies Bifidobacterium longum subsp. longum and Bifidobacterium longum subsp. infantis, which are often found in infants and adults. The increasing numbers of sequenced genomes belonging to these two subspecies, and the availability of novel computational tools focused on predicting glycolytic abilities, with the aim of understanding the capabilities of degrading specific carbohydrates, allowed us to depict the potential glycoside hydrolases (GH) of these bacteria, with a focus on those GH profiles that differ in the two subspecies. We performed an in silico examination of 188 sequenced B. longum genomes and depicted the commonly present and strain-specific GHs and GH families among representatives of this species. Additionally, GH profiling, genome-based and 16S rRNA-based clustering analyses showed that the subspecies assignment of some strains does not properly match with their genetic background. Furthermore, the analysis of the potential GH component allowed the distinction of clear GH patterns. Some of the GH activities, and their link with the two subspecies under study, are further discussed. Overall, our in silico analysis poses some questions about the suitability of considering the GH activities of B. longum subsp. longum and B. longum subsp. infantis to gain insight into the characterization and classification of these two subspecies with probiotic interest.
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Affiliation(s)
- Guillermo Blanco
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain; (G.B.); (F.F.-R.)
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Hector Tamés
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Patricia Ruas-Madiedo
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Florentino Fdez-Riverola
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain; (G.B.); (F.F.-R.)
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312 Vigo, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
| | - Anália Lourenço
- Escuela Superior de Ingeniería Informática, Edificio Politécnico, Campus Universitario As Lagoas s/n, University of Vigo, 32004 Ourense, Spain; (G.B.); (F.F.-R.)
- CINBIO-Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310 Vigo, Spain
- SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312 Vigo, Spain
- CEB-Centre of Biological Engineering, University of Minho, Campus de Campus de Gualtar, 4710-057 Braga, Portugal
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Instituto de Productos Lácteos de Asturias (IPLA), Consejo Superior de Investigaciones Científicas (CSIC), Paseo Río Linares S/N, Villaviciosa, 33300 Asturias, Spain; (H.T.); (P.R.-M.); (B.S.); (A.M.)
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, 33011 Asturias, Spain
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13
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Comparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum. Microorganisms 2019; 8:microorganisms8010007. [PMID: 31861401 PMCID: PMC7022738 DOI: 10.3390/microorganisms8010007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 12/22/2022] Open
Abstract
Bifidobacterium longum colonizes mammalian gastrointestinal tracts where it could metabolize host-indigestible oligosaccharides. Although B. longum strains are currently segregated into three subspecies that reflect common metabolic capacities and genetic similarity, heterogeneity within subspecies suggests that these taxonomic boundaries may not be completely resolved. To address this, the B. longum pangenome was analyzed from representative strains isolated from a diverse set of sources. As a result, the B. longum pangenome is open and contains almost 17,000 genes, with over 85% of genes found in ≤28 of 191 strains. B. longum genomes share a small core gene set of only ~500 genes, or ~3% of the total pangenome. Although the individual B. longum subspecies pangenomes share similar relative abundances of clusters of orthologous groups, strains show inter- and intrasubspecies differences with respect to carbohydrate utilization gene content and growth phenotypes.
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14
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Genome Sequence and Biochemical Properties of Bifidobacterium longum Strain ICIS-505, Isolated from the Intestine of a Healthy Woman. Microbiol Resour Announc 2019; 8:8/33/e00491-19. [PMID: 31416861 PMCID: PMC6696636 DOI: 10.1128/mra.00491-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This report describes the genome sequence of Bifidobacterium longum strain ICIS-505, isolated from human feces. The size of the genome was 2,448,844 bp (59.71% G+C content), including 3,751 bp of the crypto-plasmid pBL505. Annotation revealed 2,241 gene sequences, including 2,033 proteins, 7 rRNA genes, 76 tRNA genes, and 4 noncoding RNA genes. This report describes the genome sequence of Bifidobacterium longum strain ICIS-505, isolated from human feces. The size of the genome was 2,448,844 bp (59.71% G+C content), including 3,751 bp of the crypto-plasmid pBL505. Annotation revealed 2,241 gene sequences, including 2,033 proteins, 7 rRNA genes, 76 tRNA genes, and 4 noncoding RNA genes.
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15
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Mining Lactobacillus and Bifidobacterium for organisms with long-term gut colonization potential. Clin Nutr 2019; 39:1315-1323. [PMID: 31174942 DOI: 10.1016/j.clnu.2019.05.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/01/2019] [Accepted: 05/17/2019] [Indexed: 11/20/2022]
Abstract
Probiotics administered orally endure one of two fates: some merely pass through, but others colonize the gut permanently. Although probiotics that can stably engraft in the gut are believed to exert beneficial effects on the host in terms of increasing the efficiency of metabolic activity and enabling durable modulation of the indigenous microbiota, the strains of long-term gut colonizers are poorly delineated. This review summarizes the gut colonization modes of Lactobacillus and Bifidobacterium in the context of their natural niches and engraftment metadata in an attempt to identify organisms with long-term gut colonization potential. Advances in colonization evaluation methods are identified, and the effects of dietary components and metabolic interactions among ingested strains on bacterial colonization are discussed.
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16
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17
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Huang CH, Li SW, Huang L, Watanabe K. Identification and Classification for the Lactobacillus casei Group. Front Microbiol 2018; 9:1974. [PMID: 30186277 PMCID: PMC6113361 DOI: 10.3389/fmicb.2018.01974] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan.,Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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18
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Draft Genome Sequence of Bifidobacterium longum UMA026, Isolated from Holstein Dairy Cow Feces. GENOME ANNOUNCEMENTS 2018; 6:6/25/e00559-18. [PMID: 29930064 PMCID: PMC6013606 DOI: 10.1128/genomea.00559-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The draft genome sequence of an isolate identified as Bifidobacterium longum is communicated herein. This strain was isolated from the feces of a 1-week-old Holstein dairy cow. The draft genome of this Bifidobacterium longum isolate is 2.39 Mb in length, with a G+C content of 60.1%.
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19
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Odamaki T, Bottacini F, Kato K, Mitsuyama E, Yoshida K, Horigome A, Xiao JZ, van Sinderen D. Genomic diversity and distribution of Bifidobacterium longum subsp. longum across the human lifespan. Sci Rep 2018; 8:85. [PMID: 29311585 PMCID: PMC5758520 DOI: 10.1038/s41598-017-18391-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 12/11/2017] [Indexed: 12/13/2022] Open
Abstract
Bifidobacterium longum subsp. longum represents one of the most prevalent bifidobacterial species in the infant, adult and elderly (human) gut. In the current study, we performed a comparative genome analysis involving 145 B. longum representatives, including 113 B. longum subsp. longum strains obtained from healthy Japanese subjects aged between 0 and 98 years. Although MCL clustering did not reveal any correlation between isolated strains and subject age, certain characteristics appear to be more prevalent among strains corresponding to specific host ages, such as genes involved in carbohydrate metabolism and environmental response. Remarkably, a substantial number of strains appeared to have been transmitted across family members, a phenomenon that was shown not to be confined to mother-infant pairs. This suggests that the ubiquitous distribution of B. longum subsp. longum across the human lifespan is at least partly due to extensive transmission between relatives. Our findings form a foundation for future research aimed at unraveling the mechanisms that allow B. longum strains to successfully transfer between human hosts, where they then colonize and persist in the gut environment throughout the host's lifespan.
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Affiliation(s)
- Toshitaka Odamaki
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan. .,APC Microbiome Institute and School of Microbiology, National University of Ireland, Western Road, Cork, Ireland.
| | - Francesca Bottacini
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Western Road, Cork, Ireland
| | - Kumiko Kato
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Eri Mitsuyama
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Keisuke Yoshida
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Ayako Horigome
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Jin-Zhong Xiao
- Next Generation Science Institute, Morinaga Milk Industry Co., Ltd, Zama, Kanagawa, Japan
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Western Road, Cork, Ireland
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20
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Arboleya S, Bottacini F, O'Connell-Motherway M, Ryan CA, Ross RP, van Sinderen D, Stanton C. Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains. BMC Genomics 2018; 19:33. [PMID: 29310579 PMCID: PMC5759876 DOI: 10.1186/s12864-017-4388-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/15/2017] [Indexed: 12/15/2022] Open
Abstract
Background Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach. Results We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO). Conclusions The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome. Electronic supplementary material The online version of this article (10.1186/s12864-017-4388-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Paseo Río Linares, Villaviciosa, Asturias, Spain
| | - Francesca Bottacini
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Mary O'Connell-Motherway
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - C Anthony Ryan
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Department of Neonatology, Cork University Maternity Hospital, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Institute, University College Cork, Cork, Ireland.,School of Microbiology, University College Cork, Cork, Ireland
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland. .,Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland.
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21
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Modesto M, Michelini S, Sansosti MC, De Filippo C, Cavalieri D, Qvirist L, Andlid T, Spiezio C, Sandri C, Pascarelli S, Sgorbati B, Mattarelli P. Bifidobacterium callitrichidarum sp. nov. from the faeces of the emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2017; 68:141-148. [PMID: 29116036 DOI: 10.1099/ijsem.0.002472] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Three Gram-stain-positive, non-spore-forming, microaerophilic and fructose-6-phosphate phosphoketolase positive strains were isolated from a faecal sample of an adult subject of the emperor tamarin (Saguinus imperator). Given that the isolates revealed identical BOX PCR profiles, strain TRI 5T was selected as a representative and characterized further. Comparative analysis of 16S rRNA gene sequence similarity revealed that strain TRI 5T was closely related to Bifidobacterium saguini DSM 23967T (96.4 %) and to Bifidobacterium longum subsp. longum ATCC 15708 (96.2 %). Multilocus sequence analyses of five housekeeping genes showed the close phylogenetic relatedness of this strain to Bifidobacterium breve DSM 20213T (hsp60 94.1 %), Bifidobacterium saguini DSM 23967T (clpC 91 %), Bifidobacterium avesanii DSM 100685T (dnaG 80.3 %), Bifidobacterium longumsubsp. infantis ATCC 15697T (dnaJ 85.3 %) and Bifidobacterium longumsubsp. longum ATCC 15708 (rpoB 93 %), respectively. The peptidoglycan type was A3β, with an interpeptide bridge comprising l-Orn (Lys) - l-Ser - l-Ala - l-Thr - l-Ala. The DNA G+C content of strain TRI 5T was 60.9 mol%. Based on the data provided, strain TRI 5T represents a novel species of the genus Bifidobacterium for which the name Bifidobacteriumcallitrichidarum sp. nov. is proposed. The type strain is TRI 5T (=DSM 103152T=JCM 31790T).
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Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza della Manifattura 1, 38068 Rovereto (TN), Italy
| | - Maria Cristina Sansosti
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Carlotta De Filippo
- Institute of Agricultural Biology and Biotechnology, National Research Council (CNR), Via Moruzzi, 156124 Pisa, Italy
| | - Duccio Cavalieri
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
| | - Linnea Qvirist
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Thomas Andlid
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden
| | - Caterina Spiezio
- Parco Natura Viva Garda Zoological Park S.r.l, Località Figara 40, 37012 Bussolengo (VR), Italy
| | - Camillo Sandri
- Parco Natura Viva Garda Zoological Park S.r.l, Località Figara 40, 37012 Bussolengo (VR), Italy
| | - Stefano Pascarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.,Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35121 Padova, Italy
| | - Barbara Sgorbati
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.,School of Pharmacy, Biotechnology and Sport Science, Viale Berti Pichat 10, 40100 Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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22
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Pechar R, Killer J, Mekadim C, Geigerová M, Rada V. Classification of Culturable Bifidobacterial Population from Colonic Samples of Wild Pigs (Sus scrofa) Based on Three Molecular Genetic Methods. Curr Microbiol 2017; 74:1324-1331. [PMID: 28756573 DOI: 10.1007/s00284-017-1320-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/25/2017] [Indexed: 12/24/2022]
Abstract
Occurrence of bifidobacteria, known as health-promoting probiotic microorganisms, in the digestive tract of wild pigs (Sus scrofa) has not been examined yet. One hundred forty-nine fructose-6-phosphate phosphoketolase positive bacterial strains were isolated from colonic content of twenty-two individuals of wild pigs originated from four localities in the Czechia. Based on PCR-DGGE technique targeting the variable V3 region of the 16S rRNA genes, strains were initially differentiated into four groups represented by: (i) probably a new Bifidobacterium species (89 strains), (ii) B. boum/B. thermophilum/B. thermacidophilum subsp. porcinum/B. thermacidophilum subsp. thermacidophilum (sub)species (49 strains), (iii) Pseudoscardovia suis (7 strains), and (iv) B. pseudolongum subsp. globosum/B. pseudolongum subsp. pseudolongum (4 strains), respectively. Given the fact that DGGE technique did not allow to differentiate the representatives of thermophilic bifidobacteria and B. pseudolongum subspecies, strains were further classified by the 16S rRNA and thrS gene sequences. Primers targeting the variable regions of the latter gene were designed to be applicable in identification and phylogeny of Bifidobacteriaceae family. The 16S rRNA-derived phylogenetic study classified members of the first group into five subgroups in a separated cluster of thermophilic bifidobacteria. Comparable results were obtained by the thrS-derived phylogenetic analysis. Remarkably, variability among thrS sequences was higher compared with 16S rRNA gene sequences. Overall, molecular genetic techniques application allowed to identify a new Bifidobacterium phylotype which is predominant in the digestive tract of examined wild pigs.
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Affiliation(s)
- Radko Pechar
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic.,Food Research Institute Prague, Radiová 1285/7, Hostivař, 102 00, Prague 10, Czech Republic
| | - Jiří Killer
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic. .,Institute of Animal Physiology and Genetics v.v.i, Czech Academy of Sciences, Vídeňská 1083, Krč, 142 20, Prague 4, Czech Republic.
| | - Chahrazed Mekadim
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Martina Geigerová
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
| | - Vojtěch Rada
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamýcká 129, Suchdol, 165 00, Prague 6, Czech Republic
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Pechar R, Killer J, Salmonová H, Geigerová M, Švejstil R, Švec P, Sedláček I, Rada V, Benada O. Bifidobacterium apri sp. nov., a thermophilic actinobacterium isolated from the digestive tract of wild pigs (Sus scrofa). Int J Syst Evol Microbiol 2017; 67:2349-2356. [DOI: 10.1099/ijsem.0.001956] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- R. Pechar
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - J. Killer
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
- Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Vídeňská 1083, Prague 4 – Krč, 142 20, Czech Republic
| | - H. Salmonová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - M. Geigerová
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - R. Švejstil
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - P. Švec
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - I. Sedláček
- Czech Collection of Microorganisms, Masaryk University, Faculty of Science, Kamenice 5, building A25, 625 00, Brno, Czech Republic
| | - V. Rada
- Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Faculty of Agrobiology, Food and Natural Resources, Kamýcká 129, Prague 6 – Suchdol, 165 21, Czech Republic
| | - O. Benada
- Institute of Microbiology of the Czech Academy of Sciences, v.v.i., Vídeňská 1083, 142 20, Prague 4, Czech Republic
- Department of Biology, Faculty of Science, J. E. Purkyně University in Ústi nad Labem, Za Válcovnou 1000/8, 400 96 Ústí nad Labem, Czech Republic
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Jarocki P, Podleśny M, Komoń-Janczara E, Kucharska J, Glibowska A, Targoński Z. Comparison of various molecular methods for rapid differentiation of intestinal bifidobacteria at the species, subspecies and strain level. BMC Microbiol 2016; 16:159. [PMID: 27449060 PMCID: PMC4957357 DOI: 10.1186/s12866-016-0779-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 07/15/2016] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Members of the genus Bifidobacterium are anaerobic Gram-positive Actinobacteria, which are natural inhabitants of human and animal gastrointestinal tract. Certain bifidobacteria are frequently used as food additives and probiotic pharmaceuticals, because of their various health-promoting properties. Due to the enormous demand on probiotic bacteria, manufacture of high-quality products containing living microorganisms requires rapid and accurate identification of specific bacteria. Additionally, isolation of new industrial bacteria from various environments may lead to multiple isolations of the same strain, therefore, it is important to apply rapid, low-cost and effective procedures differentiating bifidobacteria at the intra-species level. The identification of new isolates using microbiological and biochemical methods is difficult, but the accurate characterization of isolated strains may be achieved using a polyphasic approach that includes classical phenotypic methods and molecular procedures. However, some of these procedures are time-consuming and cumbersome, particularly when a large group of new isolates is typed, while some other approaches may have too low discriminatory power to distinguish closely related isolates obtained from similar sources. RESULTS This work presents the evaluation of the discriminatory power of four molecular methods (ARDRA, RAPD-PCR, rep-PCR and SDS-PAGE fingerprinting) that are extensively used for fast differentiation of bifidobacteria up to the strain level. Our experiments included 17 reference strains and showed that in comparison to ARDRA, genotypic fingerprinting procedures (RAPD and rep-PCR) seemed to be less reproducible, however, they allowed to differentiate the tested microorganisms even at the intra-species level. In general, RAPD and rep-PCR have similar discriminatory power, though, in some instances more than one oligonucleotide needs to be used in random amplified polymorphic DNA analysis. Moreover, the results also demonstrated a high discriminatory power of SDS-PAGE fingerprinting of whole-cell proteins. On the other hand, the protein profiles obtained were rather complex, and therefore, difficult to analyze. CONCLUSIONS Among the tested procedures, rep-PCR proved to be the most effective and reliable method allowing rapid differentiation of Bifidobacterium strains. Additionally, the use of the BOXA1R primer in the differentiation of 21 Bifidobacterium strains, newly isolated from infant feces, demonstrated slightly better discriminatory power in comparison to PCR reactions with the (GTG)5 oligonucleotide. Thus, BOX-PCR turned out to be the most appropriate and convenient molecular technique in differentiating Bifidobacterium strains at all taxonomic levels.
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Affiliation(s)
- Piotr Jarocki
- Department of Biotechnology, Human Nutrition and Food Commodities, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland.
| | - Marcin Podleśny
- Department of Biotechnology, Human Nutrition and Food Commodities, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Human Nutrition and Food Commodities, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | - Jagoda Kucharska
- Department of Biotechnology, Human Nutrition and Food Commodities, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | - Agnieszka Glibowska
- Department of Biotechnology, Human Nutrition and Food Commodities, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
| | - Zdzisław Targoński
- Department of Biotechnology, Human Nutrition and Food Commodities, University of Life Sciences in Lublin, 8 Skromna St., 20-704, Lublin, Poland
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Arboleya S, Stanton C, Ryan CA, Dempsey E, Ross PR. Bosom Buddies: The Symbiotic Relationship Between Infants and Bifidobacterium longum ssp. longum and ssp. infantis. Genetic and Probiotic Features. Annu Rev Food Sci Technol 2016; 7:1-21. [PMID: 26934170 DOI: 10.1146/annurev-food-041715-033151] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The intestinal microbiota is a complex community that plays an important role in human health from the initial steps of its establishment. Its microbial composition has been suggested to result from selective pressures imposed by the host and is modulated by competition among its members. Bifidobacterium longum is one of the most abundant species of the Bifidobacterium genus in the gut microbiota of healthy breast-fed infants and adults. The recent advancements of 'omics techniques have facilitated the genetic and functional studies of different gut microbiota members. They have revealed the complex genetic pathways used to metabolize different compounds that likely contribute to the competitiveness and persistence of B. longum in the colon. The discovery of a genomic island in B. longum ssp. infantis that encodes specific enzymes for the metabolism of human milk oligosaccharides suggests a specific ecological adaptation. Moreover, B. longum is widely used as probiotic, and beneficial effects in infant health have been reported in several studies.
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Affiliation(s)
- Silvia Arboleya
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; ,
| | - Catherine Stanton
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; ,
| | - C Anthony Ryan
- Department of Paediatrics and Child Health, University College Cork, Ireland.,Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork, Ireland; ,
| | - Eugene Dempsey
- Department of Paediatrics and Child Health, University College Cork, Ireland.,Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork, Ireland; ,
| | - Paul R Ross
- APC Microbiome Institute, University College Cork, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland; , .,School of Microbiology, University College Cork, Cork, Ireland;
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26
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List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2015; 65:3763-3767. [DOI: 10.1099/ijsem.0.000632] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in the nomenclature of prokaryotes. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.
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Michelini S, Oki K, Yanokura E, Shimakawa Y, Modesto M, Mattarelli P, Biavati B, Watanabe K. Bifidobacterium myosotis sp. nov., Bifidobacterium tissieri sp. nov. and Bifidobacterium hapali sp. nov., isolated from faeces of baby common marmosets (Callithrix jacchus L.). Int J Syst Evol Microbiol 2015; 66:255-265. [PMID: 26515885 DOI: 10.1099/ijsem.0.000708] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In a previous study on bifidobacterial distribution in New World monkeys, six strains belonging to the Bifidobacteriaceae were isolated from faecal samples of baby common marmosets (Callithrix jacchus L.). All the isolates were Gram-positive-staining, anaerobic, asporogenous and fructose-6-phosphate phosphoketolase-positive. Comparative analysis of 16S rRNA gene sequences revealed relatively low levels of similarity (maximum identity 96 %) to members of the genus Bifidobacterium, and placed the isolates in three independent clusters: strains of cluster I (MRM_5.9T and MRM_5.10) and cluster III (MRM_5.18T and MRM_9.02) respectively showed 96.4 and 96.7 % 16S rRNA gene sequence similarity to Bifidobacterium callitrichos DSM 23973T, while strains of cluster II (MRM_8.14T and MRM_9.14) showed 95.4 % similarity to Bifidobacterium stellenboschense DSM 23968T. Phylogenetic analysis of partial hsp60 and clpC gene sequences supported an independent phylogenetic position of each cluster from each other and from the related type strains B. callitrichos DSM 23973T and B. stellenboschense DSM 23968T. Clusters I, II and III respectively showed DNA G+C contents of 64.9-65.1, 56.4-56.7 and 63.1-63.7 mol%. The major cellular fatty acids of MRM_5.9T were C14 : 0, C16 : 0 and C18 : 1ω9c dimethylacetal, while C16 : 0 was prominent in strains MRM_5.18T and MRM_8.14T, followed by C18 : 1ω9c and C14 : 0. Biochemical profiles and growth parameters were recorded for all the isolates. Based on the data provided, the clusters represent three novel species, for which the names Bifidobacterium myosotis sp. nov. (type strain MRM_5.9T = DSM 100196T = JCM 30796T), Bifidobacterium hapali sp. nov. (type strain MRM_8.14T = DSM 100202T = JCM 30799T) and Bifidobacterium tissieri sp. nov. (type strain MRM_5.18T = DSM 100201T = JCM 30798T) are proposed.
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Affiliation(s)
- Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Kaihei Oki
- Yakult Honsha European Research Center for Microbiology ESV, Technologie Park 4, 9052 Zwijnaarde, Belgium
| | - Emiko Yanokura
- Yakult Central Institute, 5-11 Izumi, Kunitachi, Tokyo 186-8650, Japan
| | | | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Bruno Biavati
- Institute of Earth Systems, Division of Rural Sciences & Food Systems, University of Malta, Msida, Malta
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, No. 50, Lane 155, Sec. 3, Keelung Rd, Taipei 10673, Taiwan ROC
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O'Callaghan A, Bottacini F, O'Connell Motherway M, van Sinderen D. Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems. BMC Genomics 2015; 16:832. [PMID: 26489930 PMCID: PMC4618763 DOI: 10.1186/s12864-015-1968-4] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 09/30/2015] [Indexed: 12/16/2022] Open
Abstract
Background Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits. Methods PacBio SMRT sequencing was used to determine the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree was constructed using a maximum-likelihood based approach in PhyML v3.0. M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned into pORI19 for insertion mutagenesis. Results In this study we present the complete genome sequences of two Bifidobacterium longum subsp. longum strains. Comparative analysis with thirty one publicly available B. longum genomes allowed the definition of the B. longum core and dispensable genomes. This analysis also highlighted differences in particular metabolic abilities between members of the B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic analysis of the B. longum core genome indicated the existence of a novel subspecies. Methylome data, coupled to the analysis of restriction-modification systems, allowed us to substantially increase the genetic accessibility of B. longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed mutagenesis. Conclusions Comparative genomic analysis of thirty three B. longum representatives revealed a closed pan-genome for this bifidobacterial species. Phylogenetic analysis of the B. longum core genome also provides evidence for a novel fifth B. longum subspecies. Finally, we improved genetic accessibility for the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a mutant of this strain. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1968-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- A O'Callaghan
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - F Bottacini
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - M O'Connell Motherway
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
| | - D van Sinderen
- APC Microbiome Institute & School of Microbiology, University College Cork, Western Road, Cork, Ireland.
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