1
|
Aihetanmu S, Liang Z, Zhang X, Luo B, Zhang H, Huang J, Tian F, Sun H, Ni Y. Genetic specialization of key bifidobacterial phylotypes in multiple mother-infant dyad cohorts from geographically isolated populations. Front Microbiol 2024; 15:1399743. [PMID: 39021621 PMCID: PMC11251887 DOI: 10.3389/fmicb.2024.1399743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/10/2024] [Indexed: 07/20/2024] Open
Abstract
Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. Bifidobacteria are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and in vitro carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to B. longum subsp. longum, B. breve, and B. animalis subsp. lactis, respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of Bifidobacterium phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that B. longum subsp. longum and B. breve exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of B. animalis subsp. lactis were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of Bifidobacterium species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications.
Collapse
Affiliation(s)
| | - Zhixuan Liang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Xueling Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Baolong Luo
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Huimin Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Jian Huang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Fengwei Tian
- School of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hailong Sun
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi, China
| |
Collapse
|
2
|
Jiang CS, Li CY, Gu CT. The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum. Curr Microbiol 2024; 81:168. [PMID: 38733376 DOI: 10.1007/s00284-024-03712-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 04/21/2024] [Indexed: 05/13/2024]
Abstract
In 2018, Nouioui et al. proposed that Bifidobacterium coryneforme was a later synonym of Bifidobacterium indicum on the basis of the digital DNA-DNA hybridization (dDDH) value (85.0%) between B. coryneforme LMG 18911T and B. indicum LMG 11587T. However, in the study of Scardovi et al. (1970), the type strains of B. indicum and B. coryneforme only exhibited 60% DNA-DNA hybridization value. In the present study, the genomes of B. coryneforme CGMCC 1.2279T, B. coryneforme JCM 5819T, B. indicum JCM 1302T, B. indicum CGMCC 1.2275T, B. indicum DSM 20214T, B. indicum LMG 27437T, B. indicum ATCC 25912T, B. indicum KCTC 3230T, B. indicum CCUG 34985T, were sequenced, and the taxonomic relationship between B. coryneforme and B. indicum was re-evaluated. On the basis of the results presented here, (i) ATCC 25912 and DSM 20214 deposited by Vittorio Scardovi are two different strains; (ii) the type strain of B. indicum is ATCC 25912T (= JCM 1302T = LMG 27437T = CGMCC 1.2275T = KCTC 3230T), and not DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587); (iii) B. coryneforme and B. indicum represent two different species of the genus Bifidobacterium; (iv) strain DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587) belongs to B. coryneforme.
Collapse
Affiliation(s)
- Cheng-Shan Jiang
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun Yan Li
- College of Food Science, Northeast Agricultural University, Harbin, 150030, People's Republic of China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin, 150030, People's Republic of China.
| |
Collapse
|
3
|
Lan Z, Zhang X, Xu M, Kong J, Zuo X, Wang Y, Wang C, Teng Y, Ni Y, Zhang Y. Whole-genome resequencing and transcriptional profiling association analysis revealed the intraspecies difference response to oligosaccharides utilization in Bifidobacterium animalis subsp. lactis. Front Microbiol 2024; 15:1375384. [PMID: 38659979 PMCID: PMC11041377 DOI: 10.3389/fmicb.2024.1375384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction As prebiotics, oligosaccharides are frequently combined with Bifidobacterium to develop synbiotic products. However, a highly diverse gene repertoire of Bifidobacterium is involved in sugar catabolism, and even phylogenetically close species may differ in their sugar utilization capabilities. To further explore the mechanism underlying the differences in Bifidobacterium animalis subsp. lactis oligosaccharide metabolism. Methods This study screened strains with differential oligosaccharide metabolism. Subsequently, these strains were subjected to genome-wide resequencing and RT-qPCR. Results The resequencing results indicated that the subspecies of B. animalis subsp. lactis had a high genome similarity. The RT-qPCR results revealed that glycosidase genes exhibited consistency in the phenotype of metabolism at the transcriptional level; the better the growth of the strains on the oligosaccharides, the higher was the expression of glycosidase genes related to the oligosaccharides. Our results suggested that the differences in the gene transcription levels led to intraspecies differences in the ability of the strains to metabolize oligosaccharides even when they belonged to the same subspecies. Discussion Future studies with more sample size could generalizable the conclusion to all B. animalis subsp. lactis strains, thus would lay the theoretical foundation for the utilization of the B. animalis subsp. lactis strain as probiotics and the development of synbiotic products.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Yongqing Ni
- School of Food Science and Technology, Shihezi University, Shihezi, Xinjiang Province, China
| | - Yan Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, Xinjiang Province, China
| |
Collapse
|
4
|
Jiang CS, Li CY, Gu CT. Bifidobacterium apis sp. nov., isolated from the gut of honeybee ( Apis mellifera). Int J Syst Evol Microbiol 2024; 74. [PMID: 38661726 DOI: 10.1099/ijsem.0.006358] [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: 04/26/2024] Open
Abstract
A novel bifidobacterium (designated F753-1T) was isolated from the gut of honeybee (Apis mellifera). Strain F753-1T was characterized using a polyphasic taxonomic approach. Strain F753-1T was phylogenetically related to the type strains of Bifidobacterium mizhiensis, Bifidobacterium asteroides, Bifidobacterium choladohabitans, Bifidobacterium mellis, Bifidobacterium apousia and Bifidobacterium polysaccharolyticum, having 98.4-99.8 % 16S rRNA gene sequence similarities. The phylogenomic tree indicated that strain F753-1T was most closely related to the type strains of B. mellis and B. choladohabitans. Strain F753-1T had the highest average nucleotide identity (94.1-94.5 %) and digital DNA-DNA hybridization (56.3 %) values with B. mellis Bin7NT. Acid production from amygdalin, d-fructose, gentiobiose, d-mannose, maltose, sucrose and d-xylose, activity of α-galactosidase, pyruvate utilization and hydrolysis of hippurate could differentiate strain F753-1T from B. mellis CCUG 66113T and B. choladohabitans JCM 34586T. Based upon the data obtained in the present study, a novel species, Bifidobacterium apis sp. nov., is proposed, and the type strain is F753-1T (=CCTCC AB 2023227T=JCM 36562T=LMG 33388T).
Collapse
Affiliation(s)
- Cheng-Shan Jiang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Yan Li
- College of Food Science, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| |
Collapse
|
5
|
Lordan C, Roche AK, Delsing D, Nauta A, Groeneveld A, MacSharry J, Cotter PD, van Sinderen D. Linking human milk oligosaccharide metabolism and early life gut microbiota: bifidobacteria and beyond. Microbiol Mol Biol Rev 2024; 88:e0009423. [PMID: 38206006 PMCID: PMC10966949 DOI: 10.1128/mmbr.00094-23] [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: 01/12/2024] Open
Abstract
SUMMARYHuman milk oligosaccharides (HMOs) are complex, multi-functional glycans present in human breast milk. They represent an intricate mix of heterogeneous structures which reach the infant intestine in an intact form as they resist gastrointestinal digestion. Therefore, they confer a multitude of benefits, directly and/or indirectly, to the developing neonate. Certain bifidobacterial species, being among the earliest gut colonizers of breast-fed infants, have an adapted functional capacity to metabolize various HMO structures. This ability is typically observed in infant-associated bifidobacteria, as opposed to bifidobacteria associated with a mature microbiota. In recent years, information has been gleaned regarding how these infant-associated bifidobacteria as well as certain other taxa are able to assimilate HMOs, including the mechanistic strategies enabling their acquisition and consumption. Additionally, complex metabolic interactions occur between microbes facilitated by HMOs, including the utilization of breakdown products released from HMO degradation. Interest in HMO-mediated changes in microbial composition and function has been the focal point of numerous studies, in recent times fueled by the availability of individual biosynthetic HMOs, some of which are now commonly included in infant formula. In this review, we outline the main HMO assimilatory and catabolic strategies employed by infant-associated bifidobacteria, discuss other taxa that exhibit breast milk glycan degradation capacity, and cover HMO-supported cross-feeding interactions and related metabolites that have been described thus far.
Collapse
Affiliation(s)
- Cathy Lordan
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
| | - Aoife K. Roche
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Arjen Nauta
- FrieslandCampina, Amersfoort, the Netherlands
| | | | - John MacSharry
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Fermoy, Co Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
6
|
Cheng Z, Chen J, Zhang Y, Li X, Zhang N, Liu F, Jiao Y. In Vitro Hypoglycemic Activities of Lactobacilli and Bifidobacterium Strains from Healthy Children's Sources and Their Effect on Stimulating GLP-1 Secretion in STC-1 Cells. Foods 2024; 13:519. [PMID: 38397496 PMCID: PMC10887728 DOI: 10.3390/foods13040519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
A long-term use of chemical drugs cannot cure type II diabetes mellitus (T2DM) and their numerous toxic side effects can be harmful to human health. In recent years, probiotics have emerged as a natural resource to replace chemical drugs in alleviating many human ailments. Healthy children's intestines have a lot of colonized Lactobacilli and Bifidobacterium, and these beneficial bacteria can help promote overall health. The objective of this study was to isolate potential antidiabetic probiotic strains from healthy children and evaluate their application prospects. Firstly, Lactobacillus and Bifidobacterium strains were isolated from healthy children's feces and identified by the pheS or clpC genes with their respective 16S rRNA genes. Then, hydrophobicity, artificial gastrointestinal fluid tolerance, α-Glucosidase and Dipeptidyl peptidase IV (DPP-IV) inhibitory activities of isolated strains were determined, and antioxidant activities and promoting secretion of GLP-1 in STC-1 cells of candidate strains were tested. Results showed that 6 strains of Lactobacillus and Bifidobacterium were obtained from the feces of healthy children aged 3 years, respectively, including Lacticaseibacillus paracasei L-21 and L-25, Levilactobacillus brevis L-16, Lentilactobacillus buchneri L-9, Lactiplantibacillus plantarum L-8 and L-3, Bifidobacterium bifidum 11-1 and B-84, Bifidobacterium longum subsp. longum 6-1, 6-2, B42 and B53. The hydrophobicity and auto-aggregation levels of all these strains were higher than 30% and 50%, respectively, and the decrease in the number of colonies of all strains in the artificial gastrointestinal fluid was less than 2 log CFU/mL. Strains L-3, L-8, L-9, L-21, 6-1, 11-1, B53 and B84 were selected based on their high α-glucosidase inhibitory activity and DPP-IV inhibitory activity, and results of the antioxidant capacity assay showed that the remaining strains all had intense comprehensive antioxidant activity. Additionally, Lacticaseibacillus paracasei L-21 and Bifidobacterium longum subsp. longum B-53 had the most substantial prompting effect on GLP-1 secretion in the STC-1 cell line. These results indicated that Lacticaseibacillus paracasei L-21 and Bifidobacterium longum subsp. longum B-53 could be used as a potential antidiabetic strain; thus, its application as a food supplement and drug ingredient could be recommended after in vivo mitigation of type II diabetes test.
Collapse
Affiliation(s)
- Zhiliang Cheng
- Key Laboratory of Dairy Science-Ministry of Education, Food College, Northeast Agricultural University, Harbin 150030, China; (Z.C.); (J.C.); (Y.Z.); (X.L.); (N.Z.)
| | - Jingru Chen
- Key Laboratory of Dairy Science-Ministry of Education, Food College, Northeast Agricultural University, Harbin 150030, China; (Z.C.); (J.C.); (Y.Z.); (X.L.); (N.Z.)
| | - Yulong Zhang
- Key Laboratory of Dairy Science-Ministry of Education, Food College, Northeast Agricultural University, Harbin 150030, China; (Z.C.); (J.C.); (Y.Z.); (X.L.); (N.Z.)
| | - Xinyi Li
- Key Laboratory of Dairy Science-Ministry of Education, Food College, Northeast Agricultural University, Harbin 150030, China; (Z.C.); (J.C.); (Y.Z.); (X.L.); (N.Z.)
| | - Ning Zhang
- Key Laboratory of Dairy Science-Ministry of Education, Food College, Northeast Agricultural University, Harbin 150030, China; (Z.C.); (J.C.); (Y.Z.); (X.L.); (N.Z.)
| | - Fei Liu
- Key Laboratory of Dairy Science-Ministry of Education, Food College, Northeast Agricultural University, Harbin 150030, China; (Z.C.); (J.C.); (Y.Z.); (X.L.); (N.Z.)
| | - Yuehua Jiao
- Center of Drug Safety Evaluation, Heilongjiang University of Chinese Medicine, Harbin 150040, China
| |
Collapse
|
7
|
Di Pierro F, Campedelli I, De Marta P, Fracchetti F, Del Casale A, Cavecchia I, Matera M, Cazzaniga M, Bertuccioli A, Guasti L, Zerbinati N. Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants. Microorganisms 2023; 11:1649. [PMID: 37512822 PMCID: PMC10383950 DOI: 10.3390/microorganisms11071649] [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: 05/31/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Antibiotics are one of the greatest scientific achievements of modern medicine, but excessive use is creating challenges for the future of medicine. Antibiotic resistance (AR) is thought to cause changes in bowel habits and an increased risk of gastroenteritis, but it may also increase the risk of overweight, obesity, autoimmune and atopic diseases, and a low response to vaccines and cancer, likely mediated by antibiotic-induced gut dysbiosis. Probiotic add-on therapy could partially prevent antibiotic-induced gut dysbiosis, but their antibiotic sensitivity features likely limits this potential. The EFSA (European Food Safety Authority) guidelines consider the use of probiotics whose antibiotic-resistant profile could be transferable an important hazard. Recently, a strain of B. breve (PRL2020) has shown to be resistant to amoxicillin and amoxicillin-clavulanate (AC) by applying the microdilution protocol according EFSA guidelines. After verifying that horizontal gene transfer is unlikely to take place, this feature suggests its concomitant use with these specific antibiotics. The results of our tests demonstrated that the strain PRL2020 is indeed endowed with amoxicillin- and AC-resistant properties and that it is also insensitive to ampicillin. In-depth analysis of the annotated genome sequence of B. breve PRL2020 was employed to query the Comprehensive Antibiotic Resistance Database (CARD) using Resistance Gene Identifier (RGI) software (version 5.2.1). The similarity among the AR determinants found was studied through nucleotide sequence alignment, and it was possible to verify not only the absence of genes explaining these features in the flanking regions but also the presence of genetic sequences (rpoB and erm(X)) putatively responsible for rifampicin and erythromycin resistance. Both features are not phenotypically expressed, and for these antibiotics, the strain is within the EFSA limits. Analysis of the flanking regions of these genes revealed possible mobile elements upstream and downstream only in the case of the erm(X) gene, but the features of the Insertion Sequences (IS) are described as not to cause horizontal transfer. Our findings on strain PRL2020 demonstrate that its AR profile is compatible with antibiotics when taken with the aim of reducing the risk of dysbiosis.
Collapse
Affiliation(s)
- Francesco Di Pierro
- Scientific & Research Department, Velleja Research, 20125 Milan, Italy
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | | | | | | | | | | | - Mariarosaria Matera
- Department of Pediatric Emergencies, Misericordia Hospital, 58100 Grosseto, Italy
| | | | - Alexander Bertuccioli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61122 Urbino, Italy
| | - Luigina Guasti
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Nicola Zerbinati
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| |
Collapse
|
8
|
Abstract
Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies.
Collapse
Affiliation(s)
- Marie Schöpping
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ahmad A. Zeidan
- Systems Biology, Discovery, Chr. Hansen A/S, Hørsholm, Denmark
| | - Carl Johan Franzén
- Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| |
Collapse
|
9
|
González-Vázquez R, Zúñiga-León E, Torres-Maravilla E, Leyte-Lugo M, Mendoza-Pérez F, Hernández-Delgado NC, Pérez-Pastén-Borja R, Azaola-Espinosa A, Mayorga-Reyes L. Genomic and Biochemical Characterization of Bifidobacterium pseudocatenulatum JCLA3 Isolated from Human Intestine. Microorganisms 2022; 10:2100. [PMID: 36363691 PMCID: PMC9695335 DOI: 10.3390/microorganisms10112100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 07/30/2023] Open
Abstract
Bifidobacteria have been investigated due to their mutualistic microbe-host interaction with humans throughout their life. This work aims to make a biochemical and genomic characterization of Bifidobacterium pseudocatenulatum JCLA3. By multilocus analysis, the species of B. pseudocatenulatum JCLA3 was established as pseudocatenulatum. It contains one circular genome of 2,369,863 bp with G + C content of 56.6%, no plasmids, 1937 CDSs, 54 tRNAs, 16 rRNAs, 1 tmRNA, 1 CRISPR region, and 401 operons predicted, including a CRISPR-Cas operon; it encodes an extensive number of enzymes, which allows it to utilize different carbohydrates. The ack gene was found as part of an operon formed by xfp and pta genes. Two genes of ldh were found at different positions. Chromosomally encoded resistance to ampicillin and cephalothin, non-hemolytic activity, and moderate inhibition of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 6538 were demonstrated by B. pseudocatenulatum JCLA3; it can survive 100% in simulated saliva, can tolerate primary and secondary glyco- or tauro-conjugated bile salts but not in a mix of bile; the strain did not survive at pH 1.5-5. The cbh gene coding to choloylglycine hydrolase was identified in its genome, which could be related to the ability to deconjugate secondary bile salts. Intact cells showed twice as much antioxidant activity than debris. B. pseudocatenulatum JCLA3 showed 49% of adhesion to Caco-2 cells. The genome and biochemical analysis help to elucidate further possible biotechnological applications of B. pseudocatenulatum JCLA3.
Collapse
Affiliation(s)
- Raquel González-Vázquez
- Laboratorio de Biotecnología, Departamento de Sistemas Biológicos, Unidad Xochimilco, CONACYT-Universidad Autónoma Metropolitana, Ciudad de Mexico 1100, Mexico
| | - Eduardo Zúñiga-León
- Laboratorio de Biotecnología, Departamento de Sistemas Biológicos, Unidad Xochimilco, Universidad Autónoma Metropolitana, Ciudad de Mexico 1100, Mexico
| | - Edgar Torres-Maravilla
- INRAE, AgroPArisTEch, Micalis Institute, Université Paris-Saclay, 78350 Jouy-en Josas, France
| | - Martha Leyte-Lugo
- Laboratorio de Biotecnología, Departamento de Sistemas Biológicos, Unidad Xochimilco, CONACYT-Universidad Autónoma Metropolitana, Ciudad de Mexico 1100, Mexico
| | - Felipe Mendoza-Pérez
- Laboratorio de Biotecnología, Departamento de Sistemas Biológicos, Unidad Xochimilco, Universidad Autónoma Metropolitana, Ciudad de Mexico 1100, Mexico
| | - Natalia C. Hernández-Delgado
- Laboratorio de Toxicología Molecular y Celular, Escuela Nacional de Ciencias Biológicas-Campus Zacatenco, Instituto Politécnico Nacional, Ciudad de Mexico 07738, Mexico
| | - Ricardo Pérez-Pastén-Borja
- Laboratorio de Toxicología Molecular y Celular, Escuela Nacional de Ciencias Biológicas-Campus Zacatenco, Instituto Politécnico Nacional, Ciudad de Mexico 07738, Mexico
| | - Alejandro Azaola-Espinosa
- Laboratorio de Biotecnología, Departamento de Sistemas Biológicos, Unidad Xochimilco, Universidad Autónoma Metropolitana, Ciudad de Mexico 1100, Mexico
| | - Lino Mayorga-Reyes
- Laboratorio de Biotecnología, Departamento de Sistemas Biológicos, Unidad Xochimilco, Universidad Autónoma Metropolitana, Ciudad de Mexico 1100, Mexico
| |
Collapse
|
10
|
Li TT, Zhang HX, Gu CT. Bifidobacterium mizhiense sp. nov., isolated from the gut of honeybee (Apis mellifera). Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005390] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A novel bifidobacteria (designated S053-2T) was isolated from the gut of honeybee (Apis mellifera). Strain S053-2T was characterized using a polyphasic taxonomic approach. The result of 16S rRNA gene sequence analysis indicated that strain S053-2T was phylogenetically related to the type strains of
Bifidobacterium asteroides
,
Bifidobacterium indicum
,
Bifidobacterium actinocoloniiforme
,
Bifidobacterium xylocopae
,
Bifidobacterium coryneforme
,
Bifidobacterium apousia
,
Bifidobacterium choladohabitans
and
Bifidobacterium polysaccharolyticum
, and had 95.5–99.7 % 16S rRNA gene sequence similarities. Based on the 16S rRNA gene sequence analysis, strain S053-2T was most closely related to the type strain of
B. asteroides
, having 99.7 % 16S rRNA gene sequence similarity. Strain S053-2T had relatively low (91.6–95.7 %) pheS, atpA, clpC, dnaG, fusA, glnA, glyS, hsp60, argS, pyrG and recA sequence similarities to the type strain of
B. asteroides
. Strain S053-2T had 94.5–95.3% atpA, clpC, dnaG, dnaK and pyrG sequence similarities to the type strain of
B. apousia
. The phylogenomic tree indicated that strain S053-2T belonged to the
B. asteroides
group, and was most closely related to the type strains of
B. asteroides
,
B. apousia
,
B. choladohabitans
and
B. polysaccharolyticum
, and distantly related to type strains of other phylogenetically related species in the
B. asteroides
group. Strain S053-2T shared the highest average nucleotide identity (ANI, 93.8 %), digital DNA–DNA hybridization (dDDH, 52.4 %) and average amino acid identity (AAI, 95.6%) values with
B. apousia
W8102T. Strain S053-2T shared 91.1 % ANI, 41.9 % dDDH and 92.5 % AAI values with
B. asteroides
DSM 20089T. Acid production from l-arabinose, d-xylose, d-mannose, amygdalin, cellobiose, maltose, melibiose, sucrose, raffinose, gentiobiose and l-fucose, and activity of esterase lipase (C8) and α-fucosidase could differentiate strain S053-2T from
B. asteroides
DSM 20089T. Acid production from d-mannose, maltose, sucrose, melezitose and gentiobiose, and activity of α-fucosidase could differentiate strain S053-2T from
B. apousia
W8102T. Based upon the data obtained in the present study, a novel species, Bifidobacterium mizhiense sp. nov., is proposed, and the type strain is S053-2T (=JCM 34710T=CCTCC AB 2021129T).
Collapse
Affiliation(s)
- Ting Ting Li
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Hong Xia Zhang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| |
Collapse
|
11
|
Argentini C, Fontana F, Alessandri G, Lugli GA, Mancabelli L, Ossiprandi MC, van Sinderen D, Ventura M, Milani C, Turroni F. Evaluation of Modulatory Activities of Lactobacillus crispatus Strains in the Context of the Vaginal Microbiota. Microbiol Spectr 2022; 10:e0273321. [PMID: 35266820 PMCID: PMC9045136 DOI: 10.1128/spectrum.02733-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/19/2022] [Indexed: 11/20/2022] Open
Abstract
It has been widely reported that members of the genus Lactobacillus dominate the vaginal microbiota, which is represented by the most prevalent species Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus gasseri, and Lactobacillus iners. L. crispatus is furthermore considered an important microbial biomarker due to its professed beneficial implications on vaginal health. In order to identify molecular mechanisms responsible for health-promoting activities that are believed to be elicited by L. crispatus, we performed in silico investigations of the intraspecies biodiversity of vaginal microbiomes followed by in vitro experiments involving various L. crispatus strains along with other vaginal Lactobacillus species mentioned above. Specifically, we assessed their antibacterial activities against a variety of pathogenic microorganisms that are associated with vaginal infections. Moreover, coculture experiments of L. crispatus strains showing the most antibacterial activity against different pathogens revealed distinct ecological fitness and competitive properties with regard to other microbial colonizers. Interestingly, we observed that even phylogenetically closely related L. crispatus strains possess unique features in terms of their antimicrobial activities and associated competitive abilities, which suggests that they exert marked competition and evolutionary pressure within their specific environmental niche. IMPORTANCE The human vaginal microbiota includes all microorganisms that colonize the vaginal tract. In this context, a vaginal microbiota dominated by Lactobacillus and specifically by Lactobacillus crispatus is considered a hallmark of health. The role of L. crispatus in maintaining host health is linked to its modulatory activity toward other members of the vaginal ecosystem and toward the host. In this study, in vitro experiments followed by genetic analyses of the mechanisms used by L. crispatus in colonizing the vaginal ecological niche, particularly in the production of different antimicrobial compounds, were evaluated, highlighting some intriguing novel aspects concerning the genetic variability of this species. Our results indicate that this species has adapted to its niche and may still undergo adaptation to enhance its competitiveness for niche colonization.
Collapse
Affiliation(s)
- Chiara Argentini
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Maria Cristina Ossiprandi
- Microbiome Research Hub, University of Parma, Parma, Italy
- Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| |
Collapse
|
12
|
Abstract
Over the last decade, the genomes of several Bifidobacterium strains have been sequenced, delivering valuable insights into their genetic makeup. However, bifidobacterial genomes have not yet been systematically mined for genes associated with stress response functions and their regulation. In this work, a list of 76 genes related to stress response in bifidobacteria was compiled from previous studies. The prevalence of the genes was evaluated among the genome sequences of 171 Bifidobacterium strains. Although genes of the protein quality control and DNA repair systems appeared to be highly conserved, genome-wide in silico screening for consensus sequences of putative regulators suggested that the regulation of these systems differs among phylogenetic groups. Homologs of multiple oxidative stress-associated genes are shared across species, albeit at low sequence similarity. Bee isolates were confirmed to harbor unique genetic features linked to oxygen tolerance. Moreover, most studied Bifidobacterium adolescentis and all Bifidobacterium angulatum strains lacked a set of reactive oxygen species-detoxifying enzymes, which might explain their high sensitivity to oxygen. Furthermore, the presence of some putative transcriptional regulators of stress responses was found to vary across species and strains, indicating that different regulation strategies of stress-associated gene transcription contribute to the diverse stress tolerance. The presented stress response gene profiles of Bifidobacterium strains provide a valuable knowledge base for guiding future studies by enabling hypothesis generation and the identification of key genes for further analyses. IMPORTANCE Bifidobacteria are Gram-positive bacteria that naturally inhabit diverse ecological niches, including the gastrointestinal tract of humans and animals. Strains of the genus Bifidobacterium are widely used as probiotics, since they have been associated with health benefits. In the course of their production and administration, probiotic bifidobacteria are exposed to several stressors that can challenge their survival. The stress tolerance of probiotic bifidobacteria is, therefore, an important selection criterion for their commercial application, since strains must maintain their viability to exert their beneficial health effects. As the ability to cope with stressors varies among Bifidobacterium strains, comprehensive understanding of the underlying stress physiology is required for enabling knowledge-driven strain selection and optimization of industrial-scale production processes.
Collapse
|
13
|
Aziz G, Zaidi A, Tariq M. Compositional Quality and Possible Gastrointestinal Performance of Marketed Probiotic Supplements. Probiotics Antimicrob Proteins 2022; 14:288-312. [PMID: 35199309 DOI: 10.1007/s12602-022-09931-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2022] [Indexed: 12/15/2022]
Abstract
The local pharmacies and shops are brimming with various probiotic products that herald a range of health benefits. The poor quality of probiotic products in both dosage and species is symptomatic of this multi-billion-dollar market making it difficult for consumers to single out reliable ones. This study aims to fill the potential gap in the labeling accuracy of probiotic products intended for human consumption. We describe a combinatorial approach using classical culture-dependent technique to quantify and molecular techniques (16 s rRNA gene sequencing, multilocus sequence, and ribotyping) for strain recognition of the microbial contents. The full gamut of probiotic characteristics including acid, bile and lysozyme tolerances, adhesiveness, anti-pathogenicity, and degree of safeness were performed. Their capacity to endure gastro-intestinal (GIT) stresses and select drugs was assessed in vitro. Our results forced us to declare that the local probiotic market is essentially unregulated. Almost none of the probiotic products tested met the label claim. Some (11%) have no viable cells, and a quarter (27%) showing significant inter-batch variation. A lower microbial count was typical with undesirables constituting a quarter of the total (~ 27%). Half of the products contained antibiotic-resistant strains; the unregulated use of these probiotics carries the risk of spreading antibiotic resistance to gut pathobionts. Poor tolerance to gut conditions and mediocre functionalism make the case worse. The current regulatory systems do not take this discrepancy into account. We recommend an evidence-based regular market surveillance of marketed probiotics to ensure the authenticity of the claims and product effectiveness.
Collapse
Affiliation(s)
- Ghazal Aziz
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C)-PIEAS, Faisalabad, 38000, Punjab, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, ICT, Pakistan
| | - Arsalan Zaidi
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C)-PIEAS, Faisalabad, 38000, Punjab, Pakistan.
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, ICT, Pakistan.
| | - Muhammad Tariq
- National Probiotic Laboratory, National Institute for Biotechnology and Genetic Engineering College (NIBGE-C)-PIEAS, Faisalabad, 38000, Punjab, Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, 45650, ICT, Pakistan
| |
Collapse
|
14
|
Applicability of rpoB Gene for PCR-RFLP based Discrimination of Bifidobacterial Species Isolated from Human and Animal Sources. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bifidobacteria are widely used as probiotics for their application in the development of functional food and prophylactic therapy. This has necessitated the development of a molecular approach for the genera to be widely identified up to species and subspecies level. In the current study, PCR-RFLP of the partial RNA polymerase β-subunit (rpoB) gene fragment was evaluated for differential identification of Bifidobacterium species. The rpoB gene partial sequences of 575 bp were amplified from 93 previously identified isolates collected from various sources of human and animal origin along with 12 standard reference strains. The PCR amplified products were digested with three restriction endonucleases HhaI, HinfI and BanI separately. Dendrograms constructed from the patterns of HhaI, were found to be more discriminatory and successfully differentiated all the twelve species and also at sub-species level in between B. longum subsp. longum and B. longum subsp. infantis. However, B. adolescentis and B. pseudocatenulatum group clusters were not separated and represented by one group. The groups were further discriminated by HinfI restriction digestion. A separate combination thereof may be used for inferring the classification of bifidobacterial species targeted on rpoB PCR-RFLP analysis. To our knowledge, this work is the first report based on use of rpoB PCR-RFLP for discrimination of the isolates of genus Bifidobacterium and also provides insights into specific advantages of this method over hsp60 PCR-RFLP in differentiating B. longum subsp. longum and B. longum subsp. infantis.
Collapse
|
15
|
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.
Collapse
|
16
|
Diversity of the type I-U CRISPR-Cas system in Bifidobacterium. Arch Microbiol 2021; 203:3235-3243. [PMID: 33837440 DOI: 10.1007/s00203-021-02310-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/17/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022]
Abstract
The CRISPR-Cas system is widely distributed in prokaryotes and plays an important role in the adaptive immunity of bacteria and archaea. Bifidobacterium is an important component of the intestinal flora of humans and animals, and some species of this bacterium can be employed as food additives. However, the Bifidobacterium CRISPR-Cas system has not been fully elucidated to date. In this study, the genomes of 110 strains of Bifidobacterium were employed to research the diversity of the type I-U system. The 110 strains were divided into five groups according to the genes adjacent to the CRISPR locus, including group A, B, C, D and E. Strains in the intergroup had unique species classifications and MLST types. An evolutionary tree was constructed based on the conserved cas4/cas1 fusion gene. The results showed that group A had a different evolutionary branch compared with the other groups and had a relatively low spacer number. Notably, group B, C and E had exhibited ABC transporter regulators in the genes adjacent to the CRISPR locus. ABC transporters play important roles in the exocytosis of many antibiotics and are involved in horizontal gene transfer. This mechanism may have promoted the evolution of Bifidobacterium and the horizontal gene transfer of the type I-U system, which may have promoted the generation of system diversity. In summary, our results help to elucidate the role of the type I-U system in the evolution of Bifidobacterium.
Collapse
|
17
|
Alessandri G, van Sinderen D, Ventura M. The genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host. Comput Struct Biotechnol J 2021; 19:1472-1487. [PMID: 33777340 PMCID: PMC7979991 DOI: 10.1016/j.csbj.2021.03.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 02/07/2023] Open
Abstract
Members of the genus Bifidobacterium are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.
Collapse
Affiliation(s)
- Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, University College Cork, Western Road, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| |
Collapse
|
18
|
Modesto M, Satti M, Watanabe K, Huang CH, Liou JS, Tamura T, Saito S, Mori K, Huang L, Sandri C, Spiezio C, Sgorbati B, Scarafile D, Cammà C, Ancora M, Patavino C, Arita M, Mattarelli P. Bifidobacteria in two-toed sloths ( Choloepus didactylus): phylogenetic characterization of the novel taxon Bifidobacterium choloepi sp. nov. Int J Syst Evol Microbiol 2021; 70:6115-6125. [PMID: 33052806 DOI: 10.1099/ijsem.0.004506] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Seven bifidobacterial strains were isolated from the faeces of two adult males of the two-toed sloth (Choloepus didactylus) housed in Parco Natura Viva, in Italy. Comparative sequence analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dnaG) genes revealed that these strains were classified into two clusters. On the basis of 16S rRNA gene sequence similarity, the type strain of Bifidobacterium catenulatum subsp. kashiwanohense DSM 21854T (95.4 %) was the closest neighbour to strain in Cluster I (BRDM 6T), whereas the type strain of Bifidobacterium dentium DSM 20436T (values were in the range of 98‒99.8 %) was the closest neighbour to the other six strains in Cluster II. The average nucleotide identity (ANI) values of BRDM 6T and of strains in Cluster II with the closely related type strains were 76.0 and 98.9 % (mean value) respectively. Therefore, genotyping based on the genome sequence of the strain BRDM 6T combined with phenotypic analyses clearly revealed that the strain BRDM 6T represents a novel species for which the names Bifidobacterium choloepi sp. nov. (BRDM 6T=NBRC 114053T=BCRC 81222T) is proposed.
Collapse
Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Barbara Sgorbati
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Massimo Ancora
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Claudio Patavino
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| |
Collapse
|
19
|
Exploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut. Microorganisms 2020; 9:microorganisms9010008. [PMID: 33375064 PMCID: PMC7822027 DOI: 10.3390/microorganisms9010008] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 12/14/2022] Open
Abstract
The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host–microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.
Collapse
|
20
|
Liu DD, Wang H, Gu CT. Proposal of Bifidobacterium saeculare Biavati et al. 1992 as a later heterotypic synonym of Bifidobacterium gallinarum Watabe et al. 1983 and Bifidobacterium gallinarum subsp. saeculare subsp. nov. Int J Syst Evol Microbiol 2020; 70:5964-5968. [DOI: 10.1099/ijsem.0.004474] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In 2018, Nouioui et al. transferred
Bifidobacterium gallinarum
and
Bifidobacterium saeculare
to
Bifidobacterium pullorum
as
B. pullorum
subsp.
gallinarum
and
B. pullorum
subsp.
saeculare
on the basis of digital DNA–DNA hybridization (dDDH) values. These two new subspecies were validated in the same year. However, we found that the genome (GenBank/ENA/DDBJ accession number JGZJ01000000) of
B. pullorum
used by Nouioui et al. in the dDDH analysis cannot represent
B. pullorum
. So, the taxonomic relationship between
B. gallinarum
,
B. saeculare
and
B. pullorum
should be re-examined.
B. pullorum
DSM 20433T had 88.7–89.0 % average nucleotide identity (ANI) values and 37.5–38.0 % dDDH values to the type strains of
B. gallinarum
and
B. saeculare
, respectively, less than the threshold for species demarcation, confirming that
B. pullorum
represents a different species from
B. gallinarum
and
B. saeculare
. The ANI values and dDDH values between the type strains of
B. gallinarum
and
B. saeculare
were 96.7–96.9 % and 73.0–73.3 %, respectively, greater than the threshold for species demarcation, confirming that they represent the same species. Relatively low dDDH values (less than the 79–80 % threshold for subspecies demarcation) between the type strains of
B. gallinarum
and
B. saeculare
indicated that
B. saeculare
can be considered as a subspecies of
B. gallinarum
. On the basis of the results presented here, (i)
B. gallinarum
and
B. saeculare
should not be transferred to
B. pullorum
; (ii) we propose
B. saeculare
Biavati et al. 1992 as a later heterotypic synonym of
B. gallinarum
Watabe et al. 1983 and as a new subspecies of
B. gallinarum
, for which the name
B. gallinarum
subsp. saeculare subsp. nov. is proposed.
Collapse
Affiliation(s)
- Dan Dan Liu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Hao Wang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| | - Chun Tao Gu
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, PR China
| |
Collapse
|
21
|
Bai X, Shen L, Gao X, Yu Z, Sakandar HA, Kwok LY, Sun Z. Differential structures and enterotype-like clusters of Bifidobacterium responses to probiotic fermented milk consumption across subjects using a Bifidobacterium-target procedure. Food Res Int 2020; 140:109839. [PMID: 33648165 DOI: 10.1016/j.foodres.2020.109839] [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: 07/15/2020] [Revised: 10/13/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023]
Abstract
The health-promoting attributes of bifidobacteria have piqued interest of researchers worldwide. However, scant published studies are available pertinent to bifidobacteria in microbiota/metagenomics datasets due to its intrinsic low abundance and limitations of detection methods. In this work, we designed a procedure to optimize the detection of the bifidobacterial population in complex biological samples with single-molecule real-time sequencing (SMRT) technology, including one primer pair designated as Bif-6 and a Bifidobacterium-specific database. The optimized procedure detected 14 bifidobacterial species/subspecies in ten human stool samples (2024 sequences per sample) and eight breast milk samples (3473 sequences per sample), respectively. Furthermore, by using the optimized procedure of SMRT, we investigated the effect of a 4-week-intervention of probiotic fermented milk (PFM; 200 g/day) on the gut bifidobacteria population of adults. The results showed that consuming PFM changed the structure and enterotype-like clusters of Bifidobacterium. After the consumption of PFM, the level of gut Bifidobacterium animalis increased significantly, replacing several originally dominating taxa in some subjects, including B. catenulatum, B. breve, and B. bifidum. On the other hand, B. adolescentis was, unaffectedly, the representative species in subjects having an original enterotype-like cluster of B. adolescentis. In conclusion, our work designed a procedure for detecting the bifidobacterial population in complex samples. By applying the currently designed procedure, we found that the PFM intervention changed the bifidobacterial enterotype-like cluster of some subjects, and such change was dependent on the basal bifidobacterial population.
Collapse
Affiliation(s)
- Xiaoye Bai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lingling Shen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Xu Gao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhongjie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Hafiz Arbab Sakandar
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Huhhot 010018, China.
| |
Collapse
|
22
|
Kim HB, Kim E, Yang SM, Lee S, Kim MJ, Kim HY. Development of Real-Time PCR Assay to Specifically Detect 22 Bifidobacterium Species and Subspecies Using Comparative Genomics. Front Microbiol 2020; 11:2087. [PMID: 33013760 PMCID: PMC7493681 DOI: 10.3389/fmicb.2020.02087] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/07/2020] [Indexed: 01/03/2023] Open
Abstract
Bifidobacterium species are used as probiotics to provide beneficial effects to humans. These effects are specific to some species or subspecies of Bifidobacterium. However, some Bifidobacterium species or subspecies are not distinguished because similarity of 16S rRNA and housekeeping gene sequences within Bifidobacterium species is very high. In this study, we developed a real-time polymerase chain reaction (PCR) assay to rapidly and accurately detect 22 Bifidobacterium species by selecting genetic markers using comparative genomic analysis. A total of 210 Bifidobacterium genome sequences were compared to select species- or subspecies-specific genetic markers. A phylogenetic tree based on pan-genomes generated clusters according to Bifidobacterium species or subspecies except that two strains were not grouped with their subspecies. Based on pan-genomes constructed, species- or subspecies-specific genetic markers were selected. The specificity of these markers was confirmed by aligning these genes against 210 genome sequences. Real-time PCR could detect 22 Bifidobacterium specifically. We constructed the criterion for quantification by standard curves. To further test the developed assay for commercial food products, we monitored 26 probiotic products and 7 dairy products. Real-time PCR results and labeling data were then compared. Most of these products (21/33, 63.6%) were consistent with their label claims. Some products labeled at species level only can be detected up to subspecies level through our developed assay.
Collapse
Affiliation(s)
- Hyeon-Be Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Eiseul Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Seung-Min Yang
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Shinyoung Lee
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Mi-Ju Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| | - Hae-Yeong Kim
- Department of Food Science and Biotechnology, Institute of Life Sciences and Resources, Kyung Hee University, Yongin, South Korea
| |
Collapse
|
23
|
Modesto M, Satti M, Watanabe K, Scarafile D, Huang CH, Liou JS, Tamura T, Saito S, Watanabe M, Mori K, Huang L, Sandri C, Spiezio C, Arita M, Mattarelli P. Phylogenetic characterization of two novel species of the genus Bifidobacterium: Bifidobacterium saimiriisciurei sp. nov. and Bifidobacterium platyrrhinorum sp. nov. Syst Appl Microbiol 2020; 43:126111. [PMID: 32847786 DOI: 10.1016/j.syapm.2020.126111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 12/25/2022]
Abstract
Three bifidobacterial Gram-stain-positive, non-spore forming and fructose-6-phosphate phosphoketolase-positive strains, SMA1T, SMB2 and SMA15T were isolated from the faeces of two adult males of the squirrel monkey (Saimiri sciureus). On the basis of 16S rRNA gene sequence similarities, the type strain of Bifidobacterium primatium DSM 100687T (99.3%; similarity) was the closest neighbour to strains SMA1T and SMB2, whereas the type strain of Bifidobacterium stellenboschense DSM 23968T (96.5%) was the closest neighbour to strain SMA15T. The average nucleotide identity (ANI) values of SMA1T and SAM15T with the closely related type strains were 93.7% and 88.1%, respectively. The in silico DNA‒DNA hybridization values with the closest neighbours were 53.1% and 36.9%, respectively. GC contents of strains SMA1T and SMA15T were 63.6 and 66.4 mol%, respectively. Based on the phylogenetic, genotypic and phenotypic data obtained, the strains SMA1T and SMA15T clearly represent two novel taxa within the genus Bifidobacterium for which the names Bifidobacterium saimiriisciurei sp. nov. (type strain SMA1T = BCRC 81223T = NBRC 114049T = DSM 106020T) and Bifidobacterium platyrrhinorum sp. nov. (type strain SMA15T = BCRC 81224T = NBRC 114051T = DSM 106029T) are proposed.
Collapse
Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Donatella Scarafile
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mizuki Watanabe
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Masanori Arita
- RIKEN Centerfor Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 2230-0045, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| |
Collapse
|
24
|
Duranti S, Lugli GA, Viappiani A, Mancabelli L, Alessandri G, Anzalone R, Longhi G, Milani C, Ossiprandi MC, Turroni F, Ventura M. Characterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov. Int J Syst Evol Microbiol 2020; 70:2288-2297. [PMID: 32065574 DOI: 10.1099/ijsem.0.004032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Two Bifidobacterium strains, i.e., 2176BT and 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176BT and 2177BT exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139T and Bifidobacterium bifidum LMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176BT=LMG 31469T=CCUG 73785T) and Bifidobacterium leontopitheci sp. nov. (2177BT=LMG 31471T=CCUG 73786T are proposed as novel Bifidobacterium species.
Collapse
Affiliation(s)
- Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | | | | | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Francesca Turroni
- Microbiome Research Hub, University of Parma, Parma, Italy.,Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy.,Microbiome Research Hub, University of Parma, Parma, Italy
| |
Collapse
|
25
|
Rodriguez CI, Martiny JBH. Evolutionary relationships among bifidobacteria and their hosts and environments. BMC Genomics 2020; 21:26. [PMID: 31914919 PMCID: PMC6950798 DOI: 10.1186/s12864-019-6435-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/26/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates. RESULTS We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes). CONCLUSIONS Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources. However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.
Collapse
Affiliation(s)
- Cynthia I Rodriguez
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| |
Collapse
|
26
|
Modesto M, Satti M, Watanabe K, Puglisi E, Morelli L, Huang CH, Liou JS, Miyashita M, Tamura T, Saito S, Mori K, Huang L, Sciavilla P, Sandri C, Spiezio C, Vitali F, Cavalieri D, Perpetuini G, Tofalo R, Bonetti A, Arita M, Mattarelli P. Characterization of Bifidobacterium species in feaces of the Egyptian fruit bat: Description of B. vespertilionis sp. nov. and B. rousetti sp. nov. Syst Appl Microbiol 2019; 42:126017. [PMID: 31585749 DOI: 10.1016/j.syapm.2019.126017] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 11/16/2022]
Abstract
Fifteen bifidobacterial strains were obtained from faeces of Rousettus aegyptiacus; after grouping them by RAPD PCR only eight were selected and characterized. Analysis of 16S rRNA and of five housekeeping (hsp60, rpoB, clpC, dnaJ, dna G) genes revealed that these eight strains were classified into five clusters: Cluster I (RST 8 and RST 16T), Cluster II (RST 9T and RST 27), Cluster III (RST 7 and RST 11), Cluster IV (RST 19), Cluster V (RST 17) were closest to Bifidobacterium avesanii DSM 100685T (96.3%), Bifidobacterium callitrichos DSM 23973T (99.2% and 99.7%), Bifidobacterium tissieri DSM 100201T (99.7 and 99.2%), Bifidobacterium reuteri DSM 23975 T (98.9%) and Bifidobacterium myosotis DSM 100196T (99.3%), respectively. Strains in Cluster I and strain RST 9 in Cluster II could not be placed within any recognized species while the other ones were identified as known species. The average nucleotide identity values between two novel strains, RST 16T and RST 9T and their closest relatives were lower than 79% and 89%, respectively. In silico DNA-DNA hybridization values for those closest relatives were 32.5 and 42.1%, respectively. Phenotypic and genotypic tests demonstrated that strains in Cluster I and RST 9T in Cluster II represent two novel species for which the names Bifidobacterium vespertilionis sp. nov. (RST 16T=BCRC 81138T=NBRC 113380T=DSM 106025T ; RST 8=BCRC 81135=NBRC 113377) and Bifidobacterium rousetti sp. nov. (RST 9T=BCRC 81136T=NBRC 113378T=DSM 106027T) are proposed.
Collapse
Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan; Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Edoardo Puglisi
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Lorenzo Morelli
- Department for Sustainable Food Processes, Faculty of Agricultural, Food and Environmental Sciences, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122 Piacenza, Italy
| | - Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Jong-Shian Liou
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Mika Miyashita
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Tomohiko Tamura
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satomi Saito
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Koji Mori
- Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE), 2-5-8, Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Piero Sciavilla
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Camillo Sandri
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | - Caterina Spiezio
- Department of Animal Health Care and Management, Parco Natura Viva - Garda Zoological Park, Bussolengo, Verona, Italy
| | | | | | - Giorgia Perpetuini
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Rosanna Tofalo
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Andrea Bonetti
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Masanori Arita
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy.
| |
Collapse
|
27
|
Mekadim C, Bunešová V, Vlková E, Hroncová Z, Killer J. Genetic marker-based multi-locus sequence analysis for classification, genotyping, and phylogenetics of the family Bifidobacteriaceae as an alternative approach to phylogenomics. Antonie van Leeuwenhoek 2019; 112:1785-1800. [PMID: 31368048 DOI: 10.1007/s10482-019-01307-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 07/24/2019] [Indexed: 02/07/2023]
Abstract
Bifidobacteria are widely known for their probiotic potential; however, little is known regarding the ecological significance and potential probiotic effects of the phylogenetically related 'scardovial' genera (Aeriscardovia, Alloscardovia, Bombiscardovia, Galliscardovia, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia) and Gardnerella classified with bifidobacteria within the Bifidobacteriaceae family. Accurate classification and genotyping of bacteria using certain housekeeping genes is possible, whilst current phylogenomic analyses allow for extremely precise classification. Studies of applicable genetic markers may provide results comparable to those obtained from phylogenomic analyses of the family Bifidobacteriaceae. Segments of the glyS (624 nucleotides), pheS (555 nucleotides), rpsA (630 nucleotides), and rpsB (432 nucleotides) genes and their concatenated sequence were explored. The mean glyS, pheS, rpsB and rpsA gene sequence similarities calculated for Bifidobacterium taxa were 84.8, 85.2, 90.2 and 86.8%, respectively. Interestingly, the average value of the Average Nucleotide Identity among 67 type strains of the family Bifidobacteriaceae (84.70%) calculated based on values published recently was in agreement with the average pairwise similarity (84.6%) among 75 type strains of Bifidobacteriaceae family computed in this study using the concatenated sequences of four gene fragments. Similar to phylogenomic analyses, several gene sequence and phylogenetic analyses revealed that concatenated gene regions allow for classification of Bifidobacteriaceae strains into particular phylogenetic clusters and groups. Phylogeny reconstructed from the concatenated sequences assisted in defining two novel phylogenetic groups, the Bifidobacterium psychraerophilum group consisting of B. psychraerophilum, Bifidobacterium crudilactis and Bifidobacterium aquikefiri species and the Bifidobacterium bombi group consisting of B. bombi, Bifidobacterium bohemicum and Bifidobacterium commune.
Collapse
Affiliation(s)
- Chahrazed Mekadim
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Krč, Czech Republic.,Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Věra Bunešová
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Eva Vlková
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Zuzana Hroncová
- Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic
| | - Jiří Killer
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Vídeňská 1083, Prague 4, 142 20, Krč, Czech Republic. .,Department of Microbiology, Nutrition and Dietetics, Food and Natural Resources, Faculty of Agrobiology, Czech University of Life Sciences, Kamýcká 129, Prague 6, 165 00, Suchdol, Czech Republic.
| |
Collapse
|
28
|
Bottacini F, Morrissey R, Roberts R, James K, van Breen J, Egan M, Lambert J, van Limpt K, Knol J, Motherway M, van Sinderen D. Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve. Nucleic Acids Res 2019; 46:1860-1877. [PMID: 29294107 PMCID: PMC5829577 DOI: 10.1093/nar/gkx1289] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 12/18/2017] [Indexed: 11/12/2022] Open
Abstract
Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastro-intestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species.
Collapse
Affiliation(s)
- Francesca Bottacini
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Ruth Morrissey
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | | | - Kieran James
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Justin van Breen
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Muireann Egan
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | | | | | - Jan Knol
- Nutricia Research, Utrecht, the Netherlands
- Laboratory of Microbiology, Wageningen Univerisity, Wageningen
| | - Mary O’Connell Motherway
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Institute & Department of Microbiology, National University of Ireland, Cork, Ireland
- To whom correspondence should be addressed. Tel: +353 21 4901365; Fax: +353 21 4903101;
| |
Collapse
|
29
|
Modesto M, Watanabe K, Arita M, Satti M, Oki K, Sciavilla P, Patavino C, Cammà C, Michelini S, Sgorbati B, Mattarelli P. Bifidobacterium jacchi sp. nov., isolated from the faeces of a baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2019; 69:2477-2485. [PMID: 31180316 DOI: 10.1099/ijsem.0.003518] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A novel Bifidobacterium strain, MRM 9.3T, was isolated from a faecal sample of a baby common marmoset (Callithrixjacchus). Cells were Gram-stain-positive, non-motile, non-sporulating, non-haemolytic, facultatively anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing hsp60, rpoB, clpC, dnaJ and dnaG genes) and the core genomes revealed that strain MRM 9.3T exhibited phylogenetic relatedness to Bifidobacterium myosotis DSM 100196T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain B.ifidobacterium myosotis DSM 100196T (95.6 %). The average nucleotide identity, amino acid average identity and in silico DNA-DNA hybridization values between MRM 9.3T and DSM 100196T were 79.9, 72.1 and 28.5 %, respectively. Phenotypic and genotypic features clearly showed that the strain MRM 9.3T represents a novel species, for which the name Bifidobacterium jacchi sp. nov. is proposed. The type strain is MRM 9.3T (=DSM 103362T =JCM 31788T).
Collapse
Affiliation(s)
- Monica Modesto
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC.,Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Masanori Arita
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan.,RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Maria Satti
- Department of Genetics, SOKENDAI University (National Institute of Genetics), Yata 1111, Mishima, Shizuoka 411-8540, Japan
| | - Kaihei Oki
- Yakult Honsha European Research Center for Microbiology ESV, Technologiepark 94, 9052 Zwijnaarde, Belgium
| | - Piero Sciavilla
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| | - Claudio Patavino
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Cesare Cammà
- National Reference Center for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise, Campo Boario, 64100, Teramo, Italy
| | - Samanta Michelini
- Department of Agricultural and Food Sciences, University of Bologna, Italy.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology Piazza della Manifattura 1, 38068 Rovereto (TN), Italy
| | - Barbara Sgorbati
- Department of Agricultural and Food Sciences, University of Bologna, Italy.,School of Pharmacy, Biotechnology and Sport Science, 40100 Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural and Food Sciences, University of Bologna, Italy
| |
Collapse
|
30
|
Killer J, Mekadim C, Bunešová V, Mrázek J, Hroncová Z, Vlková E. Glutamine synthetase type I (glnAI) represents a rewarding molecular marker in the classification of bifidobacteria and related genera. Folia Microbiol (Praha) 2019; 65:143-151. [PMID: 31069634 DOI: 10.1007/s12223-019-00716-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 04/29/2019] [Indexed: 01/01/2023]
Abstract
The family Bifidobacteriaceae constitutes an important phylogenetic group that particularly includes bifidobacterial taxa demonstrating proven or debated positive effects on host health. The increasingly widespread application of probiotic cultures in the twenty-first century requires detailed classification to the level of particular strains. This study aimed to apply the glutamine synthetase class I (glnAI) gene region (717 bp representing approximately 50% of the entire gene sequence) using specific PCR primers for the classification, typing, and phylogenetic analysis of bifidobacteria and closely related scardovial genera. In the family Bifidobacteriaceae, this is the first report on the use of this gene for such purposes. To achieve high-value results, almost all valid Bifidobacteriaceae type strains (75) and 15 strains isolated from various environments were evaluated. The threshold value of the glnAI gene identity among Bifidobacterium species (86.9%) was comparable to that of other phylogenetic/identification markers proposed for bifidobacteria and was much lower compared to the 16S rRNA gene. Further statistical and phylogenetic analyses suggest that the glnAI gene can be applied as a novel genetic marker in the classification, genotyping, and phylogenetic analysis of isolates belonging to the family Bifidobacteriaceae.
Collapse
Affiliation(s)
- Jiří Killer
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia. .,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia.
| | - Chahrazed Mekadim
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia.,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Věra Bunešová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics, v.v.i., Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague 4, Krč, Czechia
| | - Zuzana Hroncová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| | - Eva Vlková
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, 165 00, Prague 6, Suchdol, Czechia
| |
Collapse
|
31
|
Duranti S, Lugli GA, Napoli S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. Characterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov. Int J Syst Evol Microbiol 2019; 69:1288-1298. [PMID: 30789326 DOI: 10.1099/ijsem.0.003306] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Five Bifidobacterium strains, i.e. 2020BT, 2028BT, 2033BT, 2034BT and 2036BT, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating. Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020BT, 2028BT, 2033BT, 2034BT and 2036BT exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969T, Bifidobacterium bifidum LMG 11041T, Bifidobacterium choerinum LMG 10510T, Bifidobacterium gallicum LMG 11596T, Bifidobacterium imperatoris LMG 30297T, Bifidobacterium italicum LMG 30187T and Bifidobacterium vansinderenii LMG 30126T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium castoris sp. nov. (2020BT=LMG 30937T=CCUG 72816T), Bifidobacterium callimiconis sp. nov. (2028BT=LMG 30938T=CCUG 72814T), Bifidobacterium samirii sp. nov. (2033BT=LMG 30940T=CCUG 72817T), Bifidobacterium goeldii sp. nov. (2034BT=LMG 30939T=CCUG 72815T) and Bifidobacterium dolichotidis sp. nov. (2036BT=LMG 30941T=CCUG 72818T) are proposed as novel Bifidobacterium species.
Collapse
Affiliation(s)
- Sabrina Duranti
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Stefania Napoli
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- 2Department of Veterinary Medical Science, University of Parma, Parma, Italy
| | - Francesca Turroni
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Douwe van Sinderen
- 2Department of Veterinary Medical Science, University of Parma, Parma, Italy.,3APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- 1Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| |
Collapse
|
32
|
Hernández-Rodríguez D, Vásquez-Aguilar AA, Serio-Silva JC, Rebollar EA, Azaola-Espinosa A. Molecular detection of Bifidobacterium spp. in faeces of black howler monkeys (Alouatta pigra). J Med Primatol 2018; 48:99-105. [PMID: 30520095 DOI: 10.1111/jmp.12395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 10/31/2018] [Accepted: 11/09/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Bifidobacterium genus are considered to be beneficial bacteria for their hosts; however, knowledge about the specific species that are part of the gut microbiome of howler monkeys is scarce. Polymerase chain reaction (PCR) is a useful technique for the identification of non-cultivable or difficult to grow bacterial species. With the goal of detecting species of the genus Bifidobacterium in black howler monkeys, we used PCR on DNA derived from faecal samples. METHODS We collected and extracted DNA from 40 faecal samples. Using specific primers, we performed PCR and nested PCR to detect members of the Bifidobacterium genus and a subset of species: Bifidobacterium adolescentis, Bifidobacterium bifidum, Bifidobacterium infantis, Bifidobacterium longum and Bifidobacterium animalis subsp. animalis. RESULTS 97.5% (39/40) of the samples were positive for Bifidobacterium spp. We found B longum in 100% of the analysed samples. CONCLUSIONS This is the first report of B longum in black howler monkey faeces.
Collapse
Affiliation(s)
- Dolores Hernández-Rodríguez
- Doctorado en Ciencias Agropecuarias, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, CDMX, México.,Instituto de Ecología, A.C. Red de Biología y Conservación de Vertebrados, Xalapa, Veracruz, México
| | | | - Juan Carlos Serio-Silva
- Instituto de Ecología, A.C. Red de Biología y Conservación de Vertebrados, Xalapa, Veracruz, México
| | - Eria Alaide Rebollar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Alejandro Azaola-Espinosa
- Sistemas Biológicos, Laboratorio de Biotecnología, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, CDMX, México
| |
Collapse
|
33
|
Modesto M, Puglisi E, Bonetti A, Michelini S, Spiezio C, Sandri C, Sgorbati B, Morelli L, Mattarelli P. Bifidobacterium primatium sp. nov., Bifidobacterium scaligerum sp. nov., Bifidobacterium felsineum sp. nov. and Bifidobacterium simiarum sp. nov.: Four novel taxa isolated from the faeces of the cotton top tamarin (Saguinus oedipus) and the emperor tamarin (Saguinus imperator). Syst Appl Microbiol 2018; 41:593-603. [DOI: 10.1016/j.syapm.2018.07.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 07/27/2018] [Accepted: 07/31/2018] [Indexed: 01/14/2023]
|
34
|
Charniauskaya MI, Bukliarevich AA, Delegan YA, Akhremchuk AE, Filonov AE, Titok MA. Biodiversity of Hydrocarbon-Oxidizing Soil Bacteria from Various Climatic Zones. Microbiology (Reading) 2018. [DOI: 10.1134/s0026261718050065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
35
|
Killer J, Mekadim C, Pechar R, Bunešová V, Vlková E. The threonine-tRNA ligase gene region is applicable in classification, typing, and phylogenetic analysis of bifidobacteria. J Microbiol 2018; 56:713-721. [DOI: 10.1007/s12275-018-8167-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/26/2018] [Accepted: 06/27/2018] [Indexed: 11/27/2022]
|
36
|
Makino H. Bifidobacterial strains in the intestines of newborns originate from their mothers. BIOSCIENCE OF MICROBIOTA FOOD AND HEALTH 2018; 37:79-85. [PMID: 30370191 PMCID: PMC6200668 DOI: 10.12938/bmfh.18-011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 07/28/2018] [Indexed: 01/05/2023]
Abstract
The gastrointestinal tract is believed to be colonized rapidly with bacteria immediately from birth. The source of these intestinal microbes is an ongoing topic of interest because
increasing evidence suggests that the composition of the initial intestinal bacterial colonization strongly affects health. In particular, the source of bifidobacteria has received marked
attention because these bacteria are suggested to play a crucial role in protecting against susceptibility to diverse diseases later in life. However, the source of these microbes has
remained unclear. Recently, it was confirmed that mothers transmit their unique bifidobacterial strains to their children shortly after birth. The transmitted strains predominate during
early infancy, suggesting that maternal intestinal bifidobacteria are an important source of the infant gut microbiota. Accordingly, maintenance of a healthy, balanced gut microbiota during
pregnancy has an important positive influence on the newborn gut microbiota.
Collapse
Affiliation(s)
- Hiroshi Makino
- Yakult Central Institute, 5-11 Izumi, Kunitachi-shi, Tokyo 186-8650, Japan
| |
Collapse
|
37
|
Chen L, Wang L, Yassin AK, Zhang J, Gong J, Qi K, Ganta RR, Zhang Y, Yang Y, Han X, Wang C. Genetic characterization of extraintestinal Escherichia coli isolates from chicken, cow and swine. AMB Express 2018; 8:117. [PMID: 30019301 PMCID: PMC6049849 DOI: 10.1186/s13568-018-0646-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
Phenotypic determination of antimicrobial resistance in bacteria is very important for diagnosis and treatment, but sometimes this procedure needs further genetic evaluation. Whole-genome sequencing plays a critical role in deciphering and advancing our understanding of bacterial evolution, transmission, and surveillance of antimicrobial resistance. In this study, whole-genome sequencing was performed on nineteen clinically extraintestinal Escherichia coli isolates from chicken, cows and swine and showing different antimicrobial susceptibility. A total of 44 different genes conferring resistance to 11 classes of antimicrobials were detected in 15 of 19 E. coli isolates (78.9%), and 22 types of plasmids were detected in 15/19 (78.9%) isolates. In addition, whole-genome sequencing of these 19 isolates identified 111 potential virulence factors, and 53 of these VFDB-annotated genes were carried by all these 19 isolates. Twelve different virulence genes were identified while the most frequent ones were gad (glutamate decarboxylase), iss (increased serum survival) and lpfA (long polar fimbriae). All isolates harbored at least one of the virulence genes. The findings from comparative genomic analyses of the 19 diverse E. coli isolates in this study provided insights into molecular basis of the rising multi-drug resistance in E. coli.
Collapse
Affiliation(s)
- Li Chen
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Leyi Wang
- 0000 0004 1936 9991grid.35403.31Department of Veterinary Clinical Medicine and the Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL 61802 USA
| | - Afrah Kamal Yassin
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
- 0000 0001 0674 6207grid.9763.bDepartment of Food Hygiene and Safety, Faculty of Public and Environmental Health, University of Khartoum, Khartoum, 11115 Sudan
| | - Jilei Zhang
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Jiansen Gong
- 0000 0001 0526 1937grid.410727.7Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225009 China
| | - Kezong Qi
- 0000 0004 1760 4804grid.411389.6Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, Anhui Agricultural University, Hefei, 230036 China
| | - Roman R. Ganta
- 0000 0001 0737 1259grid.36567.31Center of Excellence for Vector-Borne Diseases (CEVBD), Department of Diagnostic Medicine/Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS 66506 USA
| | - Yuanyuan Zhang
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Yi Yang
- grid.268415.cCollege of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu 225009 China
| | - Xiangan Han
- 0000 0001 0526 1937grid.410727.7Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chengming Wang
- 0000 0001 2297 8753grid.252546.2College of Veterinary Medicine, Auburn University, Auburn, AL USA
| |
Collapse
|
38
|
Draft Genome Sequences of Bifidobacterium Strains Isolated from Dietary Supplements and Cultured Food Products. GENOME ANNOUNCEMENTS 2018; 6:6/26/e00610-18. [PMID: 29954907 PMCID: PMC6025948 DOI: 10.1128/genomea.00610-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Here, we present the genome sequences of 23 Bifidobacterium isolates from several commercially available dietary supplements and cultured food products. Strains of this genus are natural inhabitants of the mammalian mouth, gastrointestinal tract, and vagina. Here, we present the genome sequences of 23 Bifidobacterium isolates from several commercially available dietary supplements and cultured food products. Strains of this genus are natural inhabitants of the mammalian mouth, gastrointestinal tract, and vagina. Some species are considered beneficial to human health.
Collapse
|
39
|
Liu Y, Chen W, Yu Y, Zhang Q, Qu Q, Duan W, Zhao Y, Weng S, Zhao G, Dou T. Identification and characterisation of bifidobacteria in infant formula milk powder obtained from the Chinese market. Int Dairy J 2018. [DOI: 10.1016/j.idairyj.2018.01.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
40
|
Lugli GA, Mangifesta M, Duranti S, Anzalone R, Milani C, Mancabelli L, Alessandri G, Turroni F, Ossiprandi MC, van Sinderen D, Ventura M. Phylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov. Syst Appl Microbiol 2018; 41:173-183. [PMID: 29395537 DOI: 10.1016/j.syapm.2018.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 12/22/2017] [Accepted: 01/08/2018] [Indexed: 10/18/2022]
Abstract
Six Bifidobacterium strains, i.e., Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B, were isolated from domestic goose (Anser domesticus), European hamster (Cricetus cricetus), European rabbit (Oryctolagus cuniculus), emperor tamarin (Saguinus imperator) and pygmy marmoset (Callithrix pygmaea). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA, ITS-, multilocus- sequences and the core genome revealed that bifidobacterial strains Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B exhibit close phylogenetic relatedness with Bifidobacterium choerinum LMG 10510, Bifidobacterium hapali DSM 100202, Bifidobacterium saguini DSM 23967 and Bifidobacterium stellenboschense DSM 23968. Genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium anseris sp. nov. (Goo31D=LMG 30189T=CCUG 70960T), Bifidobacterium criceti sp. nov. (Ham19E=LMG 30188T=CCUG 70962T), Bifidobacterium imperatoris sp. nov. (Tam1G=LMG 30297T=CCUG 70961T), Bifidobacterium italicum sp. nov. (Rab10A=LMG 30187T=CCUG 70963T), Bifidobacterium margollesii sp. nov. (Uis1B=LMG 30296T=CCUG 70959T) and Bifidobacterium parmae sp. nov. (Uis4E=LMG 30295T=CCUG 70964T) are proposed as novel Bifidobacterium species.
Collapse
Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| |
Collapse
|
41
|
Tracking the Taxonomy of the Genus Bifidobacterium Based on a Phylogenomic Approach. Appl Environ Microbiol 2018; 84:AEM.02249-17. [PMID: 29222102 DOI: 10.1128/aem.02249-17] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/02/2017] [Indexed: 11/20/2022] Open
Abstract
For decades, bacterial taxonomy has been based on in vitro molecular biology techniques and comparison of molecular marker sequences to measure the degree of genetic similarity and deduce phylogenetic relatedness of novel bacterial species to reference microbial taxa. Due to the advent of the genomic era, access to complete bacterial genome contents has become easier, thereby presenting the opportunity to precisely investigate the overall genetic diversity of microorganisms. Here, we describe a high-accuracy phylogenomic approach to assess the taxonomy of members of the genus Bifidobacterium and identify apparent misclassifications in current bifidobacterial taxonomy. The developed method was validated by the classification of seven novel taxa belonging to the genus Bifidobacterium by employing their overall genetic content. The results of this study demonstrate the potential of this whole-genome approach to become the gold standard for phylogenomics-based taxonomic classification of bacteria.IMPORTANCE Nowadays, next-generation sequencing has given access to genome sequences of the currently known bacterial taxa. The public databases constructed by means of these new technologies allowed comparison of genome sequences between microorganisms, providing information to perform genomic, phylogenomic, and evolutionary analyses. In order to avoid misclassifications in the taxonomy of novel bacterial isolates, new (bifido)bacterial taxons should be validated with a phylogenomic assessment like the approach presented here.
Collapse
|
42
|
Killer J, Mekadim C, Pechar R, Bunešová V, Mrázek J, Vlková E. Gene encoding the CTP synthetase as an appropriate molecular tool for identification and phylogenetic study of the family Bifidobacteriaceae. Microbiologyopen 2018; 7:e00579. [PMID: 29356451 PMCID: PMC6079163 DOI: 10.1002/mbo3.579] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 12/04/2017] [Accepted: 12/07/2017] [Indexed: 02/02/2023] Open
Abstract
An alternative molecular marker with respect to the 16S rRNA gene demonstrating better identification and phylogenetic parameters has not been designed for the whole Bifidobacteriaceae family, which includes the genus Bifidobacterium and scardovial genera. Therefore, the aim of the study was to find such a gene in available genomic sequences, suggest appropriate means and conditions for asmplification and sequencing of the desired region of the selected gene in various strains of the bacterial family and verify the importance in classification and phylogeny. Specific primers flanking the variable region (~800 pb) within the pyrG gene encoding the CTP synthetase were designed by means of gene sequences retrieved from the genomes of strains belonging to the family Bifidobacteriaceae. The functionality and specificity of the primers were subsequently tested on the wild (7) and type strains of bifidobacteria (36) and scardovia (7). Comparative and phylogenetic studies based on obtained sequences revealed actual significance in classification and phylogeny of the Bifidobacteriaceae family. Gene statistics (percentages of mean sequence similarities and identical sites, mean number of nucleotide differences, P- and K-distances) and phylogenetic analyses (congruence between tree topologies, percentages of bootstrap values >50 and 70%) indicate that the pyrG gene represents an alternative identification and phylogenetic marker exhibiting higher discriminatory power among strains, (sub)species, and genera than the 16S rRNA gene. Sequences of the particular gene fragment, simply achieved through specific primers, enable more precisely to classify and evaluate phylogeny of the family Bifidobacteriaceae including, with some exceptions, health-promoting probiotic bacteria.
Collapse
Affiliation(s)
- Jiří Killer
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Prague 4 - Krč, Czechia.,Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Chahrazed Mekadim
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Radko Pechar
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Věra Bunešová
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| | - Jakub Mrázek
- Institute of Animal Physiology and Genetics of the Czech Academy of Sciences, Prague 4 - Krč, Czechia
| | - Eva Vlková
- Faculty of Agrobiology, Food and Natural Resources, Department of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Prague 6 - Suchdol, Czechia
| |
Collapse
|
43
|
Modesto M, Michelini S, Oki K, Biavati B, Watanabe K, Mattarelli P. Bifidobacterium catulorum sp. nov., a novel taxon from the faeces of the baby common marmoset (Callithrix jacchus). Int J Syst Evol Microbiol 2018; 68:575-581. [PMID: 29300153 DOI: 10.1099/ijsem.0.002545] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In our previous study based on hsp60 PCR-restriction fragment length polymorphism and 16S rRNA gene sequencing, we stated that the bifidobacterial strains isolated from the individual faecal samples of five baby common marmosets constituted different phylogenetically isolated groups of the genus Bifidobacterium. In that study, we also proposed that these isolated groups potentially represented novel species of the genus Bifidobacterium. Out of them, Bifidobacterium aesculapii, Bifidobacterium myosotis, Bifidobacterium tissieri and Bifidobacterium hapali, have been described recently. Another strain, designated MRM 8.19T, has been classified as member of the genus Bifidobacterium on the basis of positive results for fructose-6-phosphate phosphoketolase activity and analysis of partial 16S rRNA, hsp60, clpC, dnaJ, dnaG and rpoB gene sequences. Analysis of 16S rRNA and hsp60 gene sequences revealed that strain MRM 8.19T was related to B. tissieri DSM 100201T (95.8 %) and to Bifidobacterium bifidum ATCC 29521T (93.7 %), respectively. The DNA G+C composition was 63.7 mol% and the peptidoglycan structure was l-Orn(Lys)-l-Ser. Based on the phylogenetic, genotypic and phenotypic data reported, strain MRM 8.19T represents a novel taxon within the genus Bifidobacterium for which the name Bifidobacterium catulorum sp. nov. (type strain MRM 8.19T=DSM 103154T=JCM 31794T) is proposed.
Collapse
Affiliation(s)
- Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Italy
| | - Samanta Michelini
- Department of Agricultural Sciences, University of Bologna, Italy.,The Microsoft Research - University of Trento Centre for Computational and Systems Biology, Piazza della Manifattura 1, 38068 Rovereto, TN, Italy
| | - Kaihei Oki
- Yakult Honsha European Research Center for Microbiology ESV, Technologiepark 4, 9052 Zwijnaarde, Belgium
| | - Bruno Biavati
- Division of Rural Sciences and Food Systems, Institute of Earth Systems, University of Malta, Msida, Malta
| | - Koichi Watanabe
- Department of Animal Science and Technology, National Taiwan University, Taipei, Taiwan, ROC.,Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Italy
| |
Collapse
|
44
|
Assessment of Bifidobacterium Species Using groEL Gene on the Basis of Illumina MiSeq High-Throughput Sequencing. Genes (Basel) 2017; 8:genes8110336. [PMID: 29160815 PMCID: PMC5704249 DOI: 10.3390/genes8110336] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 11/15/2017] [Indexed: 11/17/2022] Open
Abstract
The next-generation high-throughput sequencing techniques have introduced a new way to assess the gut’s microbial diversity on the basis of 16S rRNA gene-based microbiota analysis. However, the precise appraisal of the biodiversity of Bifidobacterium species within the gut remains a challenging task because of the limited resolving power of the 16S rRNA gene in different species. The groEL gene, a protein-coding gene, evolves quickly and thus is useful for differentiating bifidobacteria. Here, we designed a Bifidobacterium-specific primer pair which targets a hypervariable sequence region within the groEL gene that is suitable for precise taxonomic identification and detection of all recognized species of the genus Bifidobacterium so far. The results showed that the novel designed primer set can specifically differentiate Bifidobacterium species from non-bifidobacteria, and as low as 104 cells of Bifidobacterium species can be detected using the novel designed primer set on the basis of Illumina Miseq high-throughput sequencing. We also developed a novel protocol to assess the diversity of Bifidobacterium species in both human and rat feces through high-throughput sequencing technologies using groEL gene as a discriminative marker.
Collapse
|
45
|
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).
Collapse
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
| |
Collapse
|
46
|
Duranti S, Mangifesta M, Lugli GA, Turroni F, Anzalone R, Milani C, Mancabelli L, Ossiprandi MC, Ventura M. Bifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator). Int J Syst Evol Microbiol 2017; 67:3987-3995. [DOI: 10.1099/ijsem.0.002243] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Sabrina Duranti
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marta Mangifesta
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Gabriele Andrea Lugli
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Rosaria Anzalone
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Marco Ventura
- Department of Chemistry, Laboratory of Probiogenomics, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| |
Collapse
|
47
|
Lugli GA, Milani C, Turroni F, Duranti S, Mancabelli L, Mangifesta M, Ferrario C, Modesto M, Mattarelli P, Jiří K, van Sinderen D, Ventura M. Comparative genomic and phylogenomic analyses of the Bifidobacteriaceae family. BMC Genomics 2017; 18:568. [PMID: 28764658 PMCID: PMC5540593 DOI: 10.1186/s12864-017-3955-4] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/24/2017] [Indexed: 11/26/2022] Open
Abstract
Background Members of the Bifidobacteriaceae family represent both dominant microbial groups that colonize the gut of various animals, especially during the suckling stage of their life, while they also occur as pathogenic bacteria of the urogenital tract. The pan-genome of the genus Bifidobacterium has been explored in detail in recent years, though genomics of the Bifidobacteriaceae family has not yet received much attention. Here, a comparative genomic analyses of 67 Bifidobacteriaceae (sub) species including all currently recognized genera of this family, i.e., Aeriscardovia, Alloscardovia, Bifidobacterium, Bombiscardovia, Gardnerella, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia, was performed. Furthermore, in order to include a representative of each of the 67 (currently recognized) (sub) species belonging to the Bifidobacteriaceae family, we sequenced the genomes of an additional 11 species from this family, accomplishing the most extensive comparative genomic analysis performed within this family so far. Results Phylogenomics-based analyses revealed the deduced evolutionary pathway followed by each member of the Bifidobacteriaceae family, highlighting Aeriscardovia aeriphila LMG 21773 as the deepest branch in the evolutionary tree of this family. Furthermore, functional analyses based on genome content unveil connections between a given member of the family, its carbohydrate utilization abilities and its corresponding host. In this context, bifidobacterial (sub) species isolated from humans and monkeys possess the highest relative number of acquired glycosyl hydrolase-encoding genes, probably in order to enhance their metabolic ability to utilize different carbon sources consumed by the host. Conclusions Within the Bifidobacteriaceae family, genomics of the genus Bifidobacterium has been extensively investigated. In contrast, very little is known about the genomics of members of the other eight genera of this family. In this study, we decoded the genome sequences of each member of the Bifidobacteriaceae family. Thanks to subsequent comparative genomic and phylogenetic analyses, the deduced pan-genome of this family, as well as the predicted evolutionary development of each taxon belonging to this family was assessed. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3955-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sabrina Duranti
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | | | - Chiara Ferrario
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Monica Modesto
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Paola Mattarelli
- Department of Agricultural Sciences, University of Bologna, Bologna, Italy
| | - Killer Jiří
- Department of Microbiology, Nutrition and Dietetics, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague, Czech Republic.,Institute of Animal Physiology and Genetics v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Douwe van Sinderen
- APC Microbiome Institute and School of Microbiology, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| |
Collapse
|
48
|
Isolation and species delineation of genus Bifidobacterium using PCR-RFLP of partial hsp60 gene fragment. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.02.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|
49
|
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
| |
Collapse
|
50
|
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: 0.9] [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.
Collapse
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
| |
Collapse
|