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Abstract
The neonatal body provides a range of potential habitats, such as the gut, for microbes. These sites eventually harbor microbial communities (microbiotas). A "complete" (adult) gut microbiota is not acquired by the neonate immediately after birth. Rather, the exclusive, milk-based nutrition of the infant encourages the assemblage of a gut microbiota of low diversity, usually dominated by bifidobacterial species. The maternal fecal microbiota is an important source of bacterial species that colonize the gut of infants, at least in the short-term. However, development of the microbiota is influenced by the use of human milk (breast feeding), infant formula, preterm delivery of infants, caesarean delivery, antibiotic administration, family details and other environmental factors. Following the introduction of weaning (complementary) foods, the gut microbiota develops in complexity due to the availability of a diversity of plant glycans in fruits and vegetables. These glycans provide growth substrates for the bacterial families (such as members of the Ruminococcaceae and Lachnospiraceae) that, in due course, will dominate the gut microbiota of the adult. Although current data are often fragmentary and observational, it can be concluded that the nutrition that a child receives in early life is likely to impinge not only on the development of the microbiota at that time but also on the subsequent lifelong, functional relationships between the microbiota and the human host. The purpose of this review, therefore, is to discuss the importance of promoting the assemblage of functionally robust gut microbiotas at appropriate times in early life.
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Affiliation(s)
- Gerald W. Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
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Jeong J, Yun K, Mun S, Chung WH, Choi SY, Nam YD, Lim MY, Hong CP, Park C, Ahn YJ, Han K. The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology. Sci Rep 2021; 11:1727. [PMID: 33462291 PMCID: PMC7814050 DOI: 10.1038/s41598-020-80826-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Characterizing the microbial communities inhabiting specimens is one of the primary objectives of microbiome studies. A short-read sequencing platform for reading partial regions of the 16S rRNA gene is most commonly used by reducing the cost burden of next-generation sequencing (NGS), but misclassification at the species level due to its length being too short to consider sequence similarity remains a challenge. Loop Genomics recently proposed a new 16S full-length-based synthetic long-read sequencing technology (sFL16S). We compared a 16S full-length-based synthetic long-read (sFL16S) and V3-V4 short-read (V3V4) methods using 24 human GUT microbiota samples. Our comparison analyses of sFL16S and V3V4 sequencing data showed that they were highly similar at all classification resolutions except the species level. At the species level, we confirmed that sFL16S showed better resolutions than V3V4 in analyses of alpha-diversity, relative abundance frequency and identification accuracy. Furthermore, we demonstrated that sFL16S could overcome the microbial misidentification caused by different sequence similarity in each 16S variable region through comparison the identification accuracy of Bifidobacterium, Bacteroides, and Alistipes strains classified from both methods. Therefore, this study suggests that the new sFL16S method is a suitable tool to overcome the weakness of the V3V4 method.
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Affiliation(s)
- Jinuk Jeong
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea
| | - Kyeongeui Yun
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science, Dankook University, Cheonan, 31116, Republic of Korea.,Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea
| | - Won-Hyong Chung
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Song-Yi Choi
- Department of Pathology, School of Medicine, Chungnam National University, Daejeon, 35015, Republic of Korea
| | - Young-do Nam
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea.,Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Mi Young Lim
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea
| | - Chang Pyo Hong
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - ChanHyeok Park
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Yong Ju Ahn
- Microbiome Division, Theragen Bio Co., Ltd, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea.
| | - Kyudong Han
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan, 31116, Republic of Korea. .,Department of Microbiology, College of Science and Technology, Dankook University, Cheonan, 31116, Republic of Korea.
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Verruck S, Silva KJ, de Oliveira Santeli H, Scariot MC, Venturelli GL, Prudencio ES, Arisi ACM. Bifidobacterium animalis ssp. lactis BB-12 enumeration by quantitative PCR assay in microcapsules with full-fat goat milk and inulin-type fructans. Food Res Int 2020; 133:109131. [PMID: 32466908 DOI: 10.1016/j.foodres.2020.109131] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 12/16/2022]
Abstract
The current study was conducted to develop a quantitative polymerase chain reaction (qPCR) assay for Bifidobacterium animalis ssp. lactis BB-12 quantification in microcapsules matrix with full-fat goat milk and inulin-type fructans. DNA was isolated from milk, feed solutions (before spray drying) and microcapsules (after spray drying) using DNAzol. Two primer pairs targeting Bal-23S or Tuf sequences were evaluated by qPCR. The qPCR efficiency was higher (89.5%) using the Tuf primers than Bal-23S primers (84.8%). Tuf primer pair was able to selectively detect B. animalis ssp. lactis BB-12. After, quantification of bifidobacteria in the microcapsules matrix by Tuf qPCR assay was compared to conventional enumeration by plate counting. The analysis of probiotic feed solutions and microcapsules showed higher (P < 0.05) bacterial enumeration determined by Tuf qPCR assay compared to those obtained by plate counting. This qPCR assay was considered a rapid and sensitive alternative for the quantification of B. animalis ssp. lactis BB-12 in probiotic microcapsules compared to plate counting.
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Affiliation(s)
- Silvani Verruck
- Dairy Technology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Kelly Justin Silva
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Helena de Oliveira Santeli
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Mirella Christine Scariot
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Gustavo Luiz Venturelli
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Elane Schwinden Prudencio
- Dairy Technology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil
| | - Ana Carolina Maisonnave Arisi
- Molecular Biology Laboratory, Food Science and Technology Department, Agrarian Science Center, Federal University of Santa Catarina, Rod. Admar Gonzaga, 1346, Itacorubi, 88034-001 Florianópolis, SC, Brazil.
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Galacto- and Fructo-oligosaccharides Utilized for Growth by Cocultures of Bifidobacterial Species Characteristic of the Infant Gut. Appl Environ Microbiol 2020; 86:AEM.00214-20. [PMID: 32220841 DOI: 10.1128/aem.00214-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/25/2020] [Indexed: 02/06/2023] Open
Abstract
Bifidobacterial species are common inhabitants of the gut of human infants during the period when milk is a major component of the diet. Bifidobacterium breve, Bifidobacterium bifidum, Bifidobacterium longum subspecies longum, and B. longum subspecies infantis have been detected frequently in infant feces, but B. longum subsp. infantis may be disadvantaged numerically in the gut of infants in westernized countries. This may be due to the different durations of breast milk feeding in different countries. Supplementation of the infant diet or replacement of breast milk using formula feeds is common in Western countries. Formula milks often contain galacto- and/or fructo-oligosaccharides (GOS and FOS, respectively) as additives to augment the concentration of oligosaccharides in ruminant milks, but the ability of B. longum subsp. infantis to utilize these potential growth substrates when they are in competition with other bifidobacterial species is unknown. We compared the growth and oligosaccharide utilization of GOS and FOS by bifidobacterial species in pure culture and coculture. Short-chain GOS and FOS (degrees of polymerization [DP] 2 and 3) were favored growth substrates for strains of B. bifidum and B. longum subsp. longum, whereas both B. breve and B. longum subsp. infantis had the ability to utilize both short- and longer-chain GOS and FOS (DP 2 to 6). B. breve was nevertheless numerically dominant over B. longum subsp. infantis in cocultures. This was probably related to the slower use of GOS of DP 3 by B. longum subsp. infantis, indicating that the kinetics of substrate utilization is an important ecological factor in the assemblage of gut communities.IMPORTANCE The kinds of bacteria that form the collection of microbes (the microbiota) in the gut of human infants may influence health and well-being. Knowledge of how the composition of the infant diet influences the assemblage of the bacterial collection is therefore important because dietary interventions may offer opportunities to alter the microbiota with the aim of improving health. Bifidobacterium longum subspecies infantis is a well-known bacterial species, but under modern child-rearing conditions it may be disadvantaged in the gut. Modern formula milks often contain particular oligosaccharide additives that are generally considered to support bifidobacterial growth. However, studies of the ability of various bifidobacterial species to grow together in the presence of these oligosaccharides have not been conducted. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of human nutrition on the development of the gut microbiota.
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Lawley B, Otal A, Moloney-Geany K, Diana A, Houghton L, Heath ALM, Taylor RW, Tannock GW. Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life. Appl Environ Microbiol 2019; 85:e01105-19. [PMID: 31375480 PMCID: PMC6752005 DOI: 10.1128/aem.01105-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/22/2019] [Indexed: 02/07/2023] Open
Abstract
The biological succession that occurs during the first year of life in the gut of infants in Western countries is broadly predictable in terms of the increasing complexity of the composition of microbiotas. Less information is available about microbiotas in Asian countries, where environmental, nutritional, and cultural influences may differentially affect the composition and development of the microbial community. We compared the fecal microbiotas of Indonesian (n = 204) and New Zealand (NZ) (n = 74) infants 6 to 7 months and 12 months of age. Comparisons were made by analysis of 16S rRNA gene sequences and derivation of community diversity metrics, relative abundances of bacterial families, enterotypes, and cooccurrence correlation networks. Abundances of Bifidobacterium longum subsp. infantis and B. longum subsp. longum were determined by quantitative PCR. All observations supported the view that the Indonesian and NZ infant microbiotas developed in complexity over time, but the changes were much greater for NZ infants. B. longum subsp. infantis dominated the microbiotas of Indonesian children, whereas B. longum subsp. longum was dominant in NZ children. Network analysis showed that the niche model (in which trophic adaptation results in preferential colonization) of the assemblage of microbiotas was supported in Indonesian infants, whereas the neutral (stochastic) model was supported by the development of the microbiotas of NZ infants. The results of the study show that the development of the fecal microbiota is not the same for infants in all countries, and they point to the necessity of obtaining a better understanding of the factors that control the colonization of the gut in early life.IMPORTANCE This study addresses the microbiology of a natural ecosystem (the infant bowel) for children in a rural setting in Indonesia and in an urban environment in New Zealand. Analysis of DNA sequences generated from the microbial community (microbiota) in the feces of the infants during the first year of life showed marked differences in the composition and complexity of the bacterial collections. The differences were most likely due to differences in the prevalence and duration of breastfeeding of infants in the two countries. These kinds of studies are essential for developing concepts of microbial ecology related to the influence of nutrition and environment on the development of the gut microbiota and for determining the long-term effects of microbiological events in early life on human health and well-being.
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Affiliation(s)
- Blair Lawley
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Anna Otal
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Kit Moloney-Geany
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Aly Diana
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
| | - Lisa Houghton
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
- Microbiome Otago, University of Otago, Dunedin, New Zealand
| | - Anne-Louise M Heath
- Department of Human Nutrition, University of Otago, Dunedin, New Zealand
- Microbiome Otago, University of Otago, Dunedin, New Zealand
| | - Rachael W Taylor
- Microbiome Otago, University of Otago, Dunedin, New Zealand
- Department of Medicine, University of Otago, Dunedin, New Zealand
| | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Microbiome Otago, University of Otago, Dunedin, New Zealand
- Riddet Centre of Research Excellence, Massey University, Palmerston North, New Zealand
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tuf Gene Sequence Variation in Bifidobacterium longum subsp. infantis Detected in the Fecal Microbiota of Chinese Infants. Appl Environ Microbiol 2018; 84:AEM.00336-18. [PMID: 29703739 DOI: 10.1128/aem.00336-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/20/2018] [Indexed: 12/12/2022] Open
Abstract
Members of the bacterial genus Bifidobacterium generally dominate the fecal microbiota of infants. The species Bifidobacterium longum is prevalent, but the B. longum subsp. longum and B. longum subsp. infantis strains that are known to colonize the infant bowel are not usually differentiated in microbiota investigations. These subspecies differ in their capacities to metabolize human milk oligosaccharides (HMO) and may have different ecological and symbiotic roles in humans. Quantitative PCR provides a quick analytical method by which to accurately ascertain the abundances of target species in microbiotas and microcosms. However, amplification targets in DNA extracted from samples need to be dependably differential. We evaluated the tuf gene sequence as a molecular target for quantitative PCR measurements of the abundances of B. longum subsp. infantis and B. longum subsp. longum in fecal microbiotas. This approach resulted in the detection of a tuf gene variant (operational taxonomic unit 49 [OTU49]) in Chinese infants that has sequence similarities to both B. longum subsp. infantis and B. longum subsp. longum We compared the genome sequence and growth and transcriptional characteristics of an OTU49 isolate cultured in HMO medium to those of other B. longum subsp. infantis cultures. We concluded from these studies that OTU49 belongs to B. longum subsp. infantis, that dependable quantitative PCR (qPCR) differentiation between the B. longum subspecies cannot be achieved by targeting tuf gene sequences, and that functional genes involved in carbohydrate metabolism might be better targets because they delineate ecological functions.IMPORTANCE High-throughput DNA sequencing methods and advanced bioinformatics analysis have revealed the composition and biochemical capacities of microbial communities (microbiota and microbiome), including those that inhabit the gut of human infants. However, the microbiology and function of natural ecosystems have received little attention in recent decades, so an appreciation of the dynamics of gut microbiota interactions is lacking. With respect to infants, rapid methodologies, such as quantitative PCR, are needed to determine the prevalences and proportions of different bifidobacterial species in observational and microcosm studies in order to obtain a better understanding of the dynamics of bifidobacterial nutrition and syntrophy, knowledge that might be used to manipulate the microbiota and perhaps ensure the better health of infants.
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Lawley B, Munro K, Hughes A, Hodgkinson AJ, Prosser CG, Lowry D, Zhou SJ, Makrides M, Gibson RA, Lay C, Chew C, Lee PS, Wong KH, Tannock GW. Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets. PeerJ 2017; 5:e3375. [PMID: 28560114 PMCID: PMC5446769 DOI: 10.7717/peerj.3375] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/04/2017] [Indexed: 01/16/2023] Open
Abstract
Background Members of the genus Bifidobacterium are abundant in the feces of babies during the exclusively-milk-diet period of life. Bifidobacterium longum is reported to be a common member of the infant fecal microbiota. However, B. longum is composed of three subspecies, two of which are represented in the bowel microbiota (B. longum subsp. longum; B. longum subsp. infantis). B. longum subspecies are not differentiated in many studies, so that their prevalence and relative abundances are not accurately known. This may largely be due to difficulty in assigning subspecies identity using DNA sequences of 16S rRNA or tuf genes that are commonly used in bacterial taxonomy. Methods We developed a qPCR method targeting the sialidase gene (subsp. infantis) and sugar kinase gene (subsp. longum) to differentiate the subspecies using specific primers and probes. Specificity of the primers/probes was tested by in silico, pangenomic search, and using DNA from standard cultures of bifidobacterial species. The utility of the method was further examined using DNA from feces that had been collected from infants inhabiting various geographical regions. Results A pangenomic search of the NCBI genomic database showed that the PCR primers/probes targeted only the respective genes of the two subspecies. The primers/probes showed total specificity when tested against DNA extracted from the gold standard strains (type cultures) of bifidobacterial species detected in infant feces. Use of the qPCR method with DNA extracted from the feces of infants of different ages, delivery method and nutrition, showed that subsp. infantis was detectable (0–32.4% prevalence) in the feces of Australian (n = 90), South-East Asian (n = 24), and Chinese babies (n = 91), but in all cases at low abundance (<0.01–4.6%) compared to subsp. longum (0.1–33.7% abundance; 21.4–100% prevalence). Discussion Our qPCR method differentiates B. longum subspecies longum and infantis using characteristic functional genes. It can be used as an identification aid for isolates of bifidobacteria, as well as in determining prevalence and abundance of the subspecies in feces. The method should thus be useful in ecological studies of the infant gut microbiota during early life where an understanding of the ecology of bifidobacterial species may be important in developing interventions to promote infant health.
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Affiliation(s)
- Blair Lawley
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Karen Munro
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Alan Hughes
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | | | | | - Dianne Lowry
- Dairy Goat Cooperative (NZ) Ltd., Hamilton, New Zealand
| | - Shao J Zhou
- Women's and Children's Health Research Institute, Adelaide, Australia.,School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | - Maria Makrides
- Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Robert A Gibson
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, Australia
| | | | | | | | | | - Gerald W Tannock
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand.,Riddet Institute Centre of Research Excellence, Palmerston North, New Zealand.,Microbiome Otago, University of Otago, Dunedin, New Zealand
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Mianzhi Y, Shah NP. Contemporary nucleic acid-based molecular techniques for detection, identification, and characterization of Bifidobacterium. Crit Rev Food Sci Nutr 2017; 57:987-1016. [PMID: 26565761 DOI: 10.1080/10408398.2015.1023761] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Bifidobacteria are one of the most important bacterial groups found in the gastrointestinal tract of humans. Medical and food industry researchers have focused on bifidobacteria because of their health-promoting properties. Researchers have historically relied on classic phenotypic approaches (culture and biochemical tests) for detection and identification of bifidobacteria. Those approaches still have values for the identification and detection of some bifidobacterial species, but they are often labor-intensive and time-consuming and can be problematic in differentiating closely related species. Rapid, accurate, and reliable methods for detection, identification, and characterization of bifidobacteria in a mixed bacterial population have become a major challenge. The advent of nucleic acid-based molecular techniques has significantly advanced isolation and detection of bifidobacteria. Diverse nucleic acid-based molecular techniques have been employed, including hybridization, target amplification, and fingerprinting. Certain techniques enable the detection, characterization, and identification at genus-, species-, and strains-levels, whereas others allow typing of species or strains of bifidobacteria. In this review, an overview of methodological principle, technique complexity, and application of various nucleic acid-based molecular techniques for detection, identification, and characterization of bifidobacteria is presented. Advantages and limitations of each technique are discussed, and significant findings based on particular techniques are also highlighted.
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Affiliation(s)
- Yao Mianzhi
- a Food and Nutritional Science , School of Biological Sciences, The University of Hong Kong , Hong Kong
| | - Nagendra P Shah
- a Food and Nutritional Science , School of Biological Sciences, The University of Hong Kong , Hong Kong
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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: 18] [Impact Index Per Article: 2.0] [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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Development and application of tuf gene-based PCR and PCR-DGGE methods for the detection of 16 Bifidobacterium species. J Food Drug Anal 2013. [DOI: 10.1016/j.jfda.2013.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Bunešová V, Vlková E, Killer J, Rada V, Ročková Š. Identification of Bifidobacterium strains from faeces of lambs. Small Rumin Res 2012. [DOI: 10.1016/j.smallrumres.2011.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Baffoni L, Gaggìa F, Di Gioia D, Santini C, Mogna L, Biavati B. A Bifidobacterium-based synbiotic product to reduce the transmission of C. jejuni along the poultry food chain. Int J Food Microbiol 2012; 157:156-61. [PMID: 22608658 DOI: 10.1016/j.ijfoodmicro.2012.04.024] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/26/2012] [Accepted: 04/28/2012] [Indexed: 01/19/2023]
Abstract
With the ban of dietary antimicrobial agents, the use of probiotics, prebiotics and synbiotics has attracted a great deal of attention in order to improve intestinal health and control food-borne pathogens, which is an important concern for the production of safe meat and meat products. Recently, Campylobacter jejuni has emerged as a leading bacterial cause of food-borne gastroenteritis in humans, and epidemiological evidences indicate poultry and poultry products as the main source of human infection. This work aimed at the development of a synbiotic mixture capable of modulating the gut microbiota of broiler chickens to obtain an increase of the beneficial bacteria (i.e. bifidobacteria, lactobacilli) and a competitive reduction of C. jejuni. The prebiotic compound used in the mixture was chosen after an in vivo trial: a fructooligosaccharide and a galactooligosaccharide were separately administered to broilers mixed with normal feed at a concentration of 0.5% and 3%, respectively. Quantitative PCR on DNA extracted from fecal samples revealed a significant (p<0.05) increase of Bifidobacterium spp. in broilers treated with the galactooligosaccharide, coupled to a decrease (p<0.05) of Campylobacter spp. The galactooligosaccharide was then combined with a probiotic Bifidobacterium strain (B. longum subsp. longum PCB133), possessing in vitro antimicrobial activity against C. jejuni. The strain was microencapsulated in a lipid matrix to ensure viability into the feed and resistance to stomach transit. Finally, the synbiotic mixture was administered to broiler chickens for 14 days mixed with normal feed in order to have an intake of 10(9)CFU of PCB133/day. Bifidobacterium spp., Lactobacillus spp., Campylobacter spp., B. longum subsp. longum and C. jejuni were quantified in fecal samples. PCB133 was recovered in feces of all animals. C. jejuni concentration in poultry feces was significantly (p<0.05) reduced in chickens administered with the synbiotic mixture. This study allowed to highlight the positive effect of the synbiotic approach for C. jejuni reduction in broiler chickens, which is of fundamental importance for the safety of poultry meat consumers.
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Affiliation(s)
- Loredana Baffoni
- Department of Agroenvironmental Sciences and Technologies, University of Bologna, Bologna, Italy.
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Sheu SJ, Hwang WZ, Chiang YC, Lin WH, Chen HC, Tsen HY. Use of tuf gene-based primers for the PCR detection of probiotic Bifidobacterium species and enumeration of bifidobacteria in fermented milk by cultural and quantitative real-time PCR methods. J Food Sci 2011; 75:M521-7. [PMID: 21535508 DOI: 10.1111/j.1750-3841.2010.01816.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Due to the increasing use of bifidobacteria in probiotic products, it is essential to establish a rapid method for the qualitative and quantitative assay of the bifidobacteria in commercial products. In this study, partial sequences of the tuf gene for 18 Bifidobacterium strains belonging to 14 species were determined. Alignment of these sequences showed that the similarities among these Bifidobacterium species were 82.24% to 99.72%. Based on these tuf gene sequences, 6 primer sets were designed for the polymerase chain reaction (PCR) assay of B. animalis subsp. animalis, B. animalis subsp. lactis, B. bifidum, B. breve, B. longum subsp. infantis, B. longum subsp. longum, and the genus of Bifidobacterium, respectively. These Bifidobacterium species are common probiotic species present in dairy and probiotic products. When each target Bifidobacterium spp. was assayed with the designed primers, PCR product with expected size was generated. In addition, for each target species, more than 70 bacterial strains other than the target species, including strains of other Bifidobacterium species, strains of Lactobacillus spp., Enterococcus spp., and other bacterial species, all generated negative results. PCR assay with primers specific to B. animalis subsp. lactis and B. longum subsp. longum confirmed the presence of these Bifidobacterium species in commercial yogurt products. In addition, for each product, enumeration of the bifidobacteria cells by culture method with BIM-25 agar and the quantitative real-time PCR showed similar cell counts. Such results indicated that within 15-d storage (4 °C) after manufacture, all the bifidobacteria cells originally present in yogurt products were viable and culturable during the storage.
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Affiliation(s)
- Sen-Je Sheu
- Dept. of Food Science and Biotechnology, Natl. Chung Hsing Univ., No. 250, Kuo Kuang Rd. Taichung City, Taiwan 402, Republic of China
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Delétoile A, Passet V, Aires J, Chambaud I, Butel MJ, Smokvina T, Brisse S. Species delineation and clonal diversity in four Bifidobacterium species as revealed by multilocus sequencing. Res Microbiol 2010; 161:82-90. [PMID: 20060895 DOI: 10.1016/j.resmic.2009.12.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 12/16/2009] [Accepted: 12/22/2009] [Indexed: 11/18/2022]
Abstract
The genus Bifidobacterium comprises several species that are important contributors to the gut microbiome, with some strains having beneficial health effects. Understanding the evolutionary emergence of advantageous biological properties requires knowledge of the genetic diversity and clonal structure of species. We sequenced seven housekeeping genes in 119 Bifidobacterium strains of Bifidobacterium animalis, Bifidobacterium bifidum, Bifidobacterium breve and Bifidobacterium longum. Phylogenetic analysis of concatenated sequences delineated sequence clusters that correspond to previously named taxa, and suggested that B. longum subsp. infantis is a nascent lineage emerging from within B. longum subsp. longum. Clear traces of recombination among distant bifidobacterial species indicate leaky species borders and warn against the practice of single gene-based identification. Multilocus sequence typing achieved precise strain genotyping, with discrimination indices above 99% in B. bifidum, B. breve and B. longum, providing a powerful tool for strain traceability, colonization dynamics and ecological studies. Frequent homologous recombination accelerates clonal diversification and may facilitate the transfer of biological properties among bifidobacterial strains.
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Affiliation(s)
- Alexis Delétoile
- Institut Pasteur, Genotyping of Pathogens and Public Health (PF8), 28 rue du Dr Roux, F-75724 Paris Cedex, France
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Mathys S, Lacroix C, Mini R, Meile L. PCR and real-time PCR primers developed for detection and identification of Bifidobacterium thermophilum in faeces. BMC Microbiol 2008; 8:179. [PMID: 18847469 PMCID: PMC2588598 DOI: 10.1186/1471-2180-8-179] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2008] [Accepted: 10/10/2008] [Indexed: 11/12/2022] Open
Abstract
Background Culture-independent methods based on the 16S ribosomal RNA molecule are nowadays widely used for assessment of the composition of the intestinal microbiota, in relation to host health or probiotic efficacy. Because Bifidobacterium thermophilum was only recently isolated from human faeces until now, no specific real-time PCR (qPCR) assay has been developed for detection of this species as component of the bifidobacterial community of the human intestinal flora. Results Design of specific primers and probe was achieved based on comparison of 108 published bifidobacterial 16S rDNA sequences with the recently published sequence of the human faecal isolate B. thermophilum RBL67. Specificity of the primer was tested in silico by similarity search against the sequence database and confirmed experimentally by PCR amplification on 17 Bifidobacterium strains, representing 12 different species, and two Lactobacillus strains. The qPCR assay developed was linear for B. thermophilum RBL67 DNA quantities ranging from 0.02 ng/μl to 200 ng/μl and showed a detection limit of 105 cells per gram faeces. The application of this new qPCR assay allowed to detect the presence of B. thermophilum in one sample from a 6-month old breast-fed baby among 17 human faecal samples tested. Additionally, the specific qPCR primers in combination with selective plating experiments led to the isolation of F9K9, a faecal isolate from a 4-month old breast-fed baby. The 16S rDNA sequence of this isolate is 99.93% similar to that of B. thermophilum RBL67 and confirmed the applicability of the new qPCR assay in faecal samples. Conclusion A new B. thermophilum-specific qPCR assay was developed based on species-specific target nucleotides in the 16S rDNA. It can be used to further characterize the composition of the bifidobacterial community in the human gastrointestinal tract. Until recently, B. thermophilum was considered as a species of animal origin, but here we confirm with the application of this new PCR assay the presence of B. thermophilum strains in the human gut.
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Affiliation(s)
- Sophie Mathys
- Laboratory of Food Biotechnology, Institute of Food Science and Nutrition, ETH Zurich, Switzerland.
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Isolation and identification of bifidobacteriaceae from human saliva. Appl Environ Microbiol 2008; 74:6457-60. [PMID: 18723652 DOI: 10.1128/aem.00895-08] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Bifidobacteriaceae were isolated from saliva and infected dentine by using a mupirocin-based selective medium. Of the saliva samples, 94% harbored bifids. The mean concentration (+/- the standard error) was 4.46 (+/-0.12) log(10)(CFU per ml + 1), and the predominant isolates were Bifidobacterium dentium, B. longum, Scardovia inopinata, Parascardovia denticolens, and Alloscardovia omnicolens.
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Detection of Bifidobacterium animalis subsp. lactis (Bb12) in the intestine after feeding of sows and their piglets. Appl Environ Microbiol 2008; 74:6338-47. [PMID: 18689506 DOI: 10.1128/aem.00309-08] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
A real-time PCR method has been developed to distinguish Bifidobacterium animalis subspecies in the gastrointestinal tracts of pigs. Identification of a highly conserved single-copy tuf gene encoding the elongation factor Tu involved in bacterial protein biosynthesis was used as a marker to differentiate homologous Bifidobacterium animalis subsp. lactis (strain Bb12) from Bifidobacterium animalis subsp. animalis, as well as Bifidobacterium suis, Bifidobacterium breve, Bifidobacterium longum, several species of Lactobacillus, and Enterococcus faecium. Real-time PCR detection of serially diluted DNA extracted from a pure culture of Bb12 was linear for bacterial numbers ranging from 10 to 10,000 tuf gene copies per PCR (r(2) = 0.99). Relative differences in Bb12 bacterial numbers in pigs fed daily with Bb12 were determined after detection of Bb12 tuf gene copies in DNA extracted from the intestinal contents. Piglets treated with Bb12 immediately after birth maintained a high level of Bb12 in their large intestines with continuous daily administration of Bb12. Piglets born to Bb12-treated sows during the last third of their gestation and also treated with Bb12 at birth (T/T group) had a higher number of Bb12 organisms per gram of intestinal contents compared to placebo-treated piglets born to placebo-treated sows (C/C group), Bb12-treated sows (T/C group), or piglets born to placebo sows but treated with Bb12 immediately after birth (C/T group). In addition, there was a significant increase in gene expression for Toll-like receptor 9 (TLR9) in piglets from the T/T group, with no change in TLR2 and TLR4. These findings suggest that the tuf gene represents a specific and functional marker for detecting Bifidobacterium animalis subsp. lactis strain Bb12 within the microbiota of the intestine.
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