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Mann AE, Chakraborty B, O'Connell LM, Nascimento MM, Burne RA, Richards VP. Heterogeneous lineage-specific arginine deiminase expression within dental microbiome species. Microbiol Spectr 2024; 12:e0144523. [PMID: 38411054 DOI: 10.1128/spectrum.01445-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 02/06/2024] [Indexed: 02/28/2024] Open
Abstract
Arginine catabolism by the bacterial arginine deiminase system (ADS) has anticariogenic properties through the production of ammonia, which modulates the pH of the oral environment. Given the potential protective capacity of the ADS pathway, the exploitation of ADS-competent oral microbes through pre- or probiotic applications is a promising therapeutic target to prevent tooth decay. To date, most investigations of the ADS in the oral cavity and its relation to caries have focused on indirect measures of activity or on specific bacterial groups, yet the pervasiveness and rate of expression of the ADS operon in diverse mixed microbial communities in oral health and disease remain an open question. Here, we use a multivariate approach, combining ultra-deep metatranscriptomic sequencing with paired metataxonomic and in vitro citrulline quantification to characterize the microbial community and ADS operon expression in healthy and late-stage cavitated teeth. While ADS activity is higher in healthy teeth, we identify multiple bacterial lineages with upregulated ADS activity on cavitated teeth that are distinct from those found on healthy teeth using both reference-based mapping and de novo assembly methods. Our dual metataxonomic and metatranscriptomic approach demonstrates the importance of species abundance for gene expression data interpretation and that patterns of differential expression can be skewed by low-abundance groups. Finally, we identify several potential candidate probiotic bacterial lineages within species that may be useful therapeutic targets for the prevention of tooth decay and propose that the development of a strain-specific, mixed-microbial probiotic may be a beneficial approach given the heterogeneity of taxa identified here across health groups. IMPORTANCE Tooth decay is the most common preventable chronic disease, affecting more than two billion people globally. The development of caries on teeth is primarily a consequence of acid production by cariogenic bacteria that inhabit the plaque microbiome. Other bacterial strains in the oral cavity may suppress or prevent tooth decay by producing ammonia as a byproduct of the arginine deiminase metabolic pathway, increasing the pH of the plaque biofilm. While the benefits of arginine metabolism on oral health have been extensively documented in specific bacterial groups, the prevalence and consistency of arginine deiminase system (ADS) activity among oral bacteria in a community context remain an open question. In the current study, we use a multi-omics approach to document the pervasiveness of the expression of the ADS operon in both health and disease to better understand the conditions in which ADS activity may prevent tooth decay.
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Affiliation(s)
- Allison E Mann
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Brinta Chakraborty
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Lauren M O'Connell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Marcelle M Nascimento
- Division of Operative Dentistry, Department of Restorative Dental Sciences, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Robert A Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Vincent P Richards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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O'Connell LM, Mann AE, Osagie E, Akhigbe P, Blouin T, Soule A, Obuekwe O, Omoigberale A, Burne RA, Coker MO, Richards VP. Supragingival mycobiome of HIV-exposed-but-uninfected children reflects a stronger correlation with caries-free-associated taxa compared to HIV-infected or uninfected children. Microbiol Spectr 2023; 11:e0149123. [PMID: 37874172 PMCID: PMC10715047 DOI: 10.1128/spectrum.01491-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 09/15/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Globally, caries is among the most frequent chronic childhood disease, and the fungal component of the microbial community responsible is poorly studied despite evidence that fungi contribute to increased acid production exacerbating enamel demineralization. HIV infection is another global health crisis. Perinatal HIV exposure with infection are caries risk factors; however, the caries experience in the context of perinatal HIV exposure without infection is less clear. Using high-throughput amplicon sequencing, we find taxonomic differences that become pronounced during late-stage caries. Notably, we show a stronger correlation with health-associated taxa for HIV-exposed-but-uninfected children when compared to unexposed and uninfected children. This aligns with a lower incidence of caries in primary teeth at age 6 or less for exposed yet uninfected children. Ultimately, these findings could contribute to improved risk assessment, intervention, and prevention strategies such as biofilm disruption and the informed design of pro-, pre-, and synbiotic oral therapies.
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Affiliation(s)
- Lauren M. O'Connell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Allison E. Mann
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Esosa Osagie
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Paul Akhigbe
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Thomas Blouin
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Ashlyn Soule
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Ozoemene Obuekwe
- Department of Oral and Maxillofacial Surgery, University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | - Augustine Omoigberale
- Department of Child Health, University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | - Robert A. Burne
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Modupe O. Coker
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Department of Oral Biology, School of Dental Medicine, Rutgers University, Newark, New Jersey, USA
| | - Vincent P. Richards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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Mann AE, O'Connell LM, Osagie E, Akhigbe P, Obuekwe O, Omoigberale A, Kelly C, Coker MO, Richards VP. Impact of HIV on the Oral Microbiome of Children Living in Sub-Saharan Africa, Determined by Using an rpoC Gene Fragment Metataxonomic Approach. Microbiol Spectr 2023; 11:e0087123. [PMID: 37428077 PMCID: PMC10434123 DOI: 10.1128/spectrum.00871-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023] Open
Abstract
Children living with HIV have a higher prevalence of oral diseases, including caries, but the mechanisms underlying this higher prevalence are not well understood. Here, we test the hypothesis that HIV infection is associated with a more cariogenic oral microbiome, characterized by an increase in bacteria involved in the pathogenesis of caries. We present data generated from supragingival plaques collected from 484 children representing three exposure groups: (i) children living with HIV (HI), (ii) children who were perinatally exposed but uninfected (HEU), and (iii) unexposed and therefore uninfected children (HUU). We found that the microbiome of HI children is distinct from those of HEU and HUU children and that this distinction is more pronounced in diseased teeth than healthy teeth, suggesting that the impact of HIV is more severe as caries progresses. Moreover, we report both an increase in bacterial diversity and a decrease in community similarity in our older HI cohort compared to our younger HI cohort, which may in part be a prolonged effect of HIV and/or its treatment. Finally, while Streptococcus mutans is often a dominant species in late-stage caries, it tended to be found at lower frequency in our HI cohort than in other groups. Our results highlight the taxonomic diversity of the supragingival plaque microbiome and suggest that broad and increasingly individualistic ecological shifts are responsible for the pathogenesis of caries in children living with HIV, coupled with a diverse and possibly severe impact on known cariogenic taxa that potentially exacerbates caries. IMPORTANCE Since its recognition as a global epidemic in the early 1980s, approximately 84.2 million people have been diagnosed with HIV and 40.1 million people have died from AIDS-related illnesses. The development and increased global availability of antiretroviral treatment (ART) regimens have dramatically reduced the mortality rate of HIV and AIDS, yet approximately 1.5 million new infections were reported in 2021, 51% of which are in sub-Saharan Africa. People living with HIV have a higher prevalence of caries and other chronic oral diseases, the mechanisms of which are not well understood. Here, we used a novel genetic approach to characterize the supragingival plaque microbiome of children living with HIV and compared it to the microbiomes of uninfected and perinatally exposed children to better understand the role of oral bacteria in the etiology of tooth decay in the context of HIV exposure and infection.
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Affiliation(s)
- Allison E Mann
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Lauren M O'Connell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Esosa Osagie
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Paul Akhigbe
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ozoemene Obuekwe
- University of Benin Teaching Hospital, Benin, Edo State, Nigeria
| | | | - Colton Kelly
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
- School of Dentistry, University of the Pacific, San Francisco, California, USA
| | - Modupe O Coker
- Institute of Human Virology Nigeria, Abuja, Nigeria
- Department of Oral Biology, Rutgers School of Dental Medicine, Rutgers University, Newark, New Jersey, USA
| | - Vincent P Richards
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
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Coker MO, Akhigbe P, Osagie E, Idemudia NL, Igedegbe O, Chukwumah N, Adebiyi R, Mann AE, O'Connell LM, Obuekwe O, Omoigberale A, Charurat ME, Richards VP. Dental caries and its association with the oral microbiomes and HIV in young children-Nigeria (DOMHaIN): a cohort study. BMC Oral Health 2021; 21:620. [PMID: 34863179 PMCID: PMC8642767 DOI: 10.1186/s12903-021-01944-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 11/03/2021] [Indexed: 01/04/2023] Open
Abstract
Background This study seeks to understand better the mechanisms underlying the increased risk of caries in HIV-infected school-aged Nigerian children by examining the relationship between the plaque microbiome and perinatal HIV infection and exposure. We also seek to investigate how perinatal HIV infection and exposure impact tooth-specific microbiomes' role on caries disease progression. Methods The participants in this study were children aged 4 to 11 years recruited from the University of Benin Teaching Hospital (UBTH), Nigeria, between May to November 2019. Overall, 568 children were enrolled in three groups: 189 HIV-infected (HI), 189 HIV-exposed but uninfected (HEU) and 190 HIV-unexposed and uninfected (HUU) as controls at visit 1 with a 2.99% and 4.90% attrition rate at visit 2 and visit 3 respectively. Data were obtained with standardized questionnaires. Blood samples were collected for HIV, HBV and HCV screening; CD4, CD8 and full blood count analysis; and plasma samples stored for future investigations; oral samples including saliva, buccal swabs, oropharyngeal swab, tongue swab, dental plaque were collected aseptically from participants at different study visits. Conclusions Results from the study will provide critical information on how HIV exposure, infection, and treatment, influence the oral microbiome and caries susceptibility in children. By determining the effect on community taxonomic structure and gene expression of dental microbiomes, we will elucidate mechanisms that potentially create a predisposition for developing dental caries. As future plans, the relationship between respiratory tract infections, immune and inflammatory markers with dental caries in perinatal HIV infection and exposure will be investigated. Supplementary Information The online version contains supplementary material available at 10.1186/s12903-021-01944-y.
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Affiliation(s)
- Modupe O Coker
- Department of Oral Biology, Rutgers School of Dental Medicine, Rutgers University, 110 Bergen Street, Room C-845, Newark, NJ, 07103, USA. .,Research Department, Institute of Human Virology, Nigeria, Abuja, Nigeria.
| | - Paul Akhigbe
- Research Department, Institute of Human Virology, Nigeria, Abuja, Nigeria
| | - Esosa Osagie
- Research Department, Institute of Human Virology, Nigeria, Abuja, Nigeria
| | - Nosakhare L Idemudia
- Medical Microbiology Division, Medical Laboratory Services, University of Benin Teaching Hospital, Benin City, Nigeria
| | - Oghenero Igedegbe
- Research Department, Institute of Human Virology, Nigeria, Abuja, Nigeria
| | - Nneka Chukwumah
- Department of Preventive Dentistry, University of Benin, Benin City, Nigeria
| | - Ruxton Adebiyi
- Research Department, Institute of Human Virology, Nigeria, Abuja, Nigeria
| | - Allison E Mann
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | | | - Ozo Obuekwe
- Department of Oral and Maxillofacial Surgery, University of Benin, Benin City, Nigeria
| | | | - Manhattan E Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, USA
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O'Connell LM, Mosseler A, Rajora OP. Impacts of forest fragmentation on the mating system and genetic diversity of white spruce (Picea glauca) at the landscape level. Heredity (Edinb) 2006; 97:418-26. [PMID: 16912700 DOI: 10.1038/sj.hdy.6800886] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We studied the mating system of white spruce (Picea glauca) in a landscape fragmented by agriculture in northern Ontario, Canada. We sampled 23 stands that ranged in size from 1 to >500 trees isolated by 250-3000 m from the nearest other stand. Six polymorphic allozyme loci from four enzyme systems were used to genotype approximately 10 000 embryos from 104 families. We detected no allele frequency heterogeneity in the pollen pool among stands or families (Phi(FT)=-0.025). Overall, estimates of outcrossing were high (t(m)=94% and mean t(s)=91%) but significantly different from unity. Bi-parental inbreeding (t(m)-t(s)=3.2%) was low but significantly different from zero. Allozyme-based outcrossing estimates did not differ significantly among three stand-size classes (SSCs): small (<10 trees), medium (10-100 trees) and large (> or =100 trees). The number of effective pollen donors was high in all SSCs, but was significantly lower in small stands (N(ep)=62.5) than in medium-sized and large stands (both N(ep)=143). The primary selfing rate was significantly higher in medium stands than in large stands. We found no significant difference in genetic diversity measures in the filial (seed) population among SSCs. Overall, these results indicate that white spruce stands in this fragmented landscape are resistant to genetic diversity losses, primarily through high pollen-mediated gene-flow and early selection against inbred embryos. We discuss the importance of using seed data, in conjunction with genetic data, to evaluate the impacts of fragmentation on natural populations.
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Affiliation(s)
- L M O'Connell
- Canada Research Chair in Forest and Conservation Genomics and Biotechnology, Faculty of Forestry and Environmental Management, University of New Brunswick, PO Box 44555, 28 Dineen Drive, Fredericton, New Brunswick, Canada E3B 6C2.
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Abstract
Western redcedar (Thuja plicata, Cupressaceae) is a self-fertile conifer with a mixed mating system and significant variation for outcrossing among populations. In this paper, we conducted a fine-scale study of mating system variation to identify correlates of outcrossing in natural populations. We examined variation for outcrossing within and among individual trees, and describe a new method to estimate outcrossing using bulked DNA samples. Bulking (assaying DNA tissues from several individuals simultaneously) increases the experimental power without increasing the experimental effort. We sampled 80 trees from four natural populations in southwestern British Columbia. From each tree, we sampled from up to six crown positions (three heights and inner vs outer branches). From each position, two samples of three seedlings each were bulked before DNA extractions. Using four microsatellite loci, we obtained outcrossing rates for each tree and for each of the six crown positions. We found individual tree selfing rates to increase with tree height in all four populations, but selfing rates did not differ among crown positions. The higher selfing rate of larger trees is probably due to their greater proportional contribution to local pollen clouds. Individual tree outcrossing rates ranged from 22 to 100% and the population outcrossing rates from 66 to 78%. Missed alleles due to bulking and the estimation method used both cause a downward bias in outcrossing rates, so that these estimates are probably lower than the actual outcrossing rates. Nevertheless, the trends we observed are not affected by systematic biases of estimation.
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Affiliation(s)
- L M O'Connell
- Department of Forest Sciences, 2424 Main Mall, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4.
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Abstract
A per-generation somatic mutation rate for microsatellites was estimated in western redcedar (Thuja plicata, Donn ex D. Don.: Cupressaceae). A total of 80 trees representative of the average size and age of reproductive trees were sampled in four natural populations in southwestern British Columbia. Samples of bulked haploid megagametophytes were collected from two or three positions on each tree, assuming that the collections were far enough apart that the same mutant sector was not sampled twice. All samples were genotyped at eight microsatellite loci. A single mutation corresponding to a stepwise increase in one dinucleotide repeat was detected. The estimated mutation rate for microsatellites was 6.3 x 10(-4) mutations per locus per generation (or 3.1 x 10(-4) per allele per generation), with a 95% confidence interval of 3.0 x 10(-5) to 4.0 x 10(-3) mutations per locus. Somatic mutations can contribute to a greater mutational load in trees, as compared to shorter lived plants, and genotypic mosaics within an individual have important implications for plant defense strategies and plant evolution.
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Affiliation(s)
- L M O'Connell
- Natural Resources Canada, Canadian Forest Service, Atlantic Forestry Centre, PO Box 4000, Fredericton, NB, E3B 5P7, Canada
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Affiliation(s)
- L M O'Connell
- Department of Forest Sciences, 2424 Main Mall, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada.
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