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Zafar H, Saier MH. Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species. Microb Physiol 2022; 32:30-44. [PMID: 34555832 PMCID: PMC8940750 DOI: 10.1159/000518954] [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: 03/07/2021] [Accepted: 08/02/2021] [Indexed: 01/03/2023]
Abstract
The human microbiome influences human health in both negative and positive ways. Studies on the transportomes of these organisms yield information that may be utilized for various purposes, including the identification of novel drug targets and the manufacture of improved probiotic strains. Moreover, these genomic analyses help to improve our understanding of the physiology and metabolic capabilities of these organisms. The present study is a continuation of our studies on the transport proteins of the major gut microbes. Bifidobacterium species are essential members of the human gut microbiome, and they initiate colonization of the gut at birth, providing health benefits that last a lifetime. In this study we analyze the transportomes of nine bifidobacterial species: B. adolescentis, B. animalis, B. bifidum, B. breve, B. catenulatum, B. dentium, B. longum subsp. infantis, B. longum subsp. longum, and B. pseudocatenulatum. All of these species have proven probiotic characteristics and exert beneficial effects on human health. Surprisingly, we found that all nine of these species have similar pore-forming toxins and drug exporters that may play roles in pathogenesis. These species have transporters for amino acids, carbohydrates, and proteins, essential for their organismal lifestyles and adaption to their respective ecological niches. The strictly probiotic species, B. bifidum, however, contains fewer such transporters, thus indicative of limited interactions with host cells and other gut microbial counterparts. The results of this study were compared with those of our previous studies on the transportomes of multiple species of Bacteroides, Escherichia coli/Salmonella, and Lactobacillus. Overall, bifidobacteria have larger transportomes (based on percentages of total proteins) than the previously examined groups of bacterial species, with a preference for primary active transport systems over secondary carriers. Taken together, these results provide useful information about the physiologies and pathogenic potentials of these probiotic organisms as reflected by their transportomes.
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Affiliation(s)
- Hassan Zafar
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116.,Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic.,Corresponding Authors HZ: Tel: +420773283624, ; MS: Tel: +1 858 534 4084, Fax: +1 858 534 7108,
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116.,Corresponding Authors HZ: Tel: +420773283624, ; MS: Tel: +1 858 534 4084, Fax: +1 858 534 7108,
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Structure of a Core Promoter in Bifidobacterium longum NCC2705. J Bacteriol 2020; 202:JB.00540-19. [PMID: 31964699 DOI: 10.1128/jb.00540-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/14/2020] [Indexed: 01/04/2023] Open
Abstract
Bacterial promoters consist of core sequence motifs termed -35 and -10 boxes. The consensus motifs are TTGACA and TATAAT, respectively, which were identified from leading investigations on Escherichia coli However, the consensus sequences are not likely to fit genetically divergent bacteria. The sigma factor of the genus Bifidobacterium has a characteristic polar domain in the N terminus, suggesting the possibility of specific promoter recognition. We reevaluated the structure of Bifidobacterium longum NCC2705 promoters and compared them to other bacteria. Transcriptional start sites (TSSs) of the B. longum NCC2705 strain were identified using transcriptome sequencing (RNA-Seq) analysis to extract promoter regions. Conserved motifs of a bifidobacterial promoter were determined using regions upstream of TSSs and a hidden Markov model. As a result, consensus motifs of the -35 and -10 boxes were TTGTGC and TACAAT, respectively. To assess each base of both motifs, we constructed 37 plasmids based on pKO403-TPCTcon, including the hup promoter connected with a chloramphenicol acetyltransferase as a reporter gene. This reporter assay showed two optimal motifs of the -35 and -10 boxes, namely, TTGNNN and TANNNT, respectively. We further analyzed spacer lengths between the -35 and -10 boxes via a bioinformatics approach. The spacer lengths predominant in bacteria have been generally reported to be approximately 17 bp. In contrast, the predominant spacer lengths in the genus Bifidobacterium and related species were 11 bp, in addition to 17 bp. A reporter assay to assess the spacer lengths indicated that the 11-bp spacer length produced unusually high activity.IMPORTANCE The structures of sigma factors vary among bacterial strains, indicating that recognition rules may also vary. Therefore, we investigated the promoter structure of Bifidobacterium longum NCC2705 using a bioinformatics approach and wet analyses. The most frequent and optimal motifs were similar to other bacterial consensus motifs. The optimal spacer length between the two boxes was reported to be 17 bp. It is widely applied to a bioinformatics approach for other bacteria. Unexpectedly, conserved spacer lengths were 11 bp as well as 17 bp in the genus Bifidobacterium Moreover, the sigma factor of the genus Bifidobacterium has a characteristic domain in the N terminus which may contribute to the additional functions. Hence, it would be valuable to reevaluate the promoter in other organisms.
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LaMonte MJ, Genco RJ, Buck MJ, McSkimming DI, Li L, Hovey KM, Andrews CA, Zheng W, Sun Y, Millen AE, Tsompana M, Banack HR, Wactawski-Wende J. Composition and diversity of the subgingival microbiome and its relationship with age in postmenopausal women: an epidemiologic investigation. BMC Oral Health 2019; 19:246. [PMID: 31722703 PMCID: PMC6854792 DOI: 10.1186/s12903-019-0906-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood. METHODS The 16S rRNA gene of subgingival plaque in 1219 women, aged 53-81 years, was sequenced and its taxonomy annotated against the Human Oral Microbiome Database (v.14.5). Composition of the subgingival microbiome was described in terms of centered log(2)-ratio (CLR) transformed OTU values, relative abundance, and prevalence. Correlations between microbiota abundance and age were evelauted using Pearson Product Moment correlations. P-values were corrected for multiple testing using the Bonferroni method. RESULTS Of the 267 species identified overall, Veillonella dispar was the most abundant bacteria when described by CLR OTU (mean 8.3) or relative abundance (mean 8.9%); whereas Streptococcus oralis, Veillonella dispar and Veillonella parvula were most prevalent (100%, all) when described as being present at any amount. Linear correlations between age and several CLR OTUs (Pearson r = - 0.18 to 0.18), of which 82 (31%) achieved statistical significance (P < 0.05). The correlations lost significance following Bonferroni correction. Twelve species that differed across age groups (each corrected P < 0.05); 5 (42%) were higher in women ages 50-59 compared to ≥70 (corrected P < 0.05), and 7 (48%) were higher in women 70 years and older. CONCLUSIONS We identified associations between several bacterial species and age across the age range of postmenopausal women studied. Understanding the functions of these bacteria could identify intervention targets to enhance oral health in later life.
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Affiliation(s)
- Michael J. LaMonte
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, 3435 Main Street, Buffalo, NY 14214 USA
| | - Robert J. Genco
- Department of Oral Biology, School of Dental Medicine, UB Microbiome Center, University at Buffalo, Buffalo, NY USA
| | - Michael J. Buck
- Department of Biochemistry, School of Medicine and Biomedical Sciences, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY USA
| | - Daniel I. McSkimming
- Genome, Environment, and Microbiome Center of Excellence, University at Buffalo, Buffalo, NY USA
| | - Lu Li
- Department of Microbiology and Immunology and Department of Computer and Engineering Science, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY USA
| | - Kathleen M. Hovey
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, 3435 Main Street, Buffalo, NY 14214 USA
| | - Christopher A. Andrews
- Department of Ophthalmology, School of Medicine, University of Michigan, Ann Arbor, MI USA
| | - Wei Zheng
- Department of Microbiology and Immunology and Department of Computer and Engineering Science, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY USA
| | - Yijun Sun
- Department of Microbiology and Immunology and Department of Computer and Engineering Science, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY USA
| | - Amy E. Millen
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, 3435 Main Street, Buffalo, NY 14214 USA
| | - Maria Tsompana
- Department of Biochemistry, School of Medicine and Biomedical Sciences, NY State Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY USA
| | - Hailey R. Banack
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, 3435 Main Street, Buffalo, NY 14214 USA
| | - Jean Wactawski-Wende
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, 270 Farber Hall, 3435 Main Street, Buffalo, NY 14214 USA
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Chenicheri S, R U, Ramachandran R, Thomas V, Wood A. Insight into Oral Biofilm: Primary, Secondary and Residual Caries and Phyto-Challenged Solutions. Open Dent J 2017; 11:312-333. [PMID: 28839480 PMCID: PMC5543615 DOI: 10.2174/1874210601711010312] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 02/15/2017] [Accepted: 03/28/2017] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Dental caries is known to be one of the most widespread, chronic infections affecting all ages and populations worldwide. The plethora of oral microbial population paves way for various endogenous infections and plays a crucial role in polymicrobial interactions contributing to biofilm-mediated diseases like caries and periodontal diseases. METHODS Extensive literature survey was conducted using the scientific databases like PubMed, Google scholar, Science Direct, etc. using the key words like dental caries, orodental infections, dental microbes, dental biofilm, secondary caries, phytotherapy, etc. The literature was analyzed thoroughly and critical review was performed. RESULTS The risk of development of secondary caries and residual caries further results in treatment failure. Drug resistance developed by oral microbes and further side effects pose serious hurdles in the current therapeutic strategies. The hyperactivities of various MMPs and the resulting massive ECM degradation are the challenging part in the design of effective therapeutic approaches. Anticariogenic phytotherapy is well appreciated owing to lesser side effects and versatility of their action. But appreciable outcomes regarding the phytochemical bioavailability and bioretention are still challenging. Site-specific delivery of phytoagents at the infected site may enhance the efficiency of these drugs. Accordingly emerging phytodentistry can be promising for the management of secondary and residual caries. CONCLUSION This article presents major cariogens and their mechanisms in initiating and aggravating dental caries. Effectiveness of phytotherapy and different mode of action of phytochemicals against cariogens are outlined. The article also raises major concerns and possibilities of phytochemical based therapeutics to be applied in the clinical arena of caries management.
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Affiliation(s)
- Smitha Chenicheri
- Department of Microbiology, Karpagam University, Coimbatore, Tamil Nadu, India.,Microbiology Division, Biogenix Research Center for Molecular Biology and Applied Sciences, Thiruvananthapuram, Kerala, India.,Department of Microbiology, PMS Dental college and Research Center, Thiruvananthapuram, Kerala, India
| | - Usha R
- Department of Microbiology, Karpagam University, Coimbatore, Tamil Nadu, India
| | - Rajesh Ramachandran
- Microbiology Division, Biogenix Research Center for Molecular Biology and Applied Sciences, Thiruvananthapuram, Kerala, India
| | - Vinoy Thomas
- Department of Materials Science & Engineering, Center for Nanoscale Materials and Biointegration (CNMB), University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
| | - Andrew Wood
- Department of Materials Science & Engineering, Center for Nanoscale Materials and Biointegration (CNMB), University of Alabama at Birmingham (UAB), Birmingham, Alabama, USA
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