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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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Mancilla VJ, Braden-Kuhle PN, Brice KN, Mann AE, Williams MT, Zhang Y, Chumley MJ, Barber RC, White SN, Boehm GW, Allen MS. A Synthetic Formula Amino Acid Diet Leads to Microbiome Dysbiosis, Reduced Colon Length, Inflammation, and Altered Locomotor Activity in C57BL/6J Mice. Microorganisms 2023; 11:2694. [PMID: 38004705 PMCID: PMC10673175 DOI: 10.3390/microorganisms11112694] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
The effects of synthetic, free-amino acid diets, similar to those prescribed as supplements for (phenylketonuria) PKU patients, on gut microbiota and overall health are not well understood. In the current, multidisciplinary study, we examined the effects of a synthetically-derived, low-fiber, amino acid diet on behavior, cognition, gut microbiome composition, and inflammatory markers. A cohort of 20 male C57BL/6J mice were randomly assigned to either a standard or synthetic diet (n = 10) at post-natal day 21 and maintained for 13 weeks. Sequencing of the 16S rRNA gene from fecal samples revealed decreased bacterial diversity, increased abundance of bacteria associated with disease, such as Prevotella, and a downward shift in gut microbiota associated with fermentation pathways in the synthetic diet group. Furthermore, there were decreased levels of short chain fatty acids and shortening of the colon in mice consuming the synthetic diet. Finally, we measured TNF-α, IL-6, and IL-10 in serum, the hippocampus, and colon, and found that the synthetic diet significantly increased IL-6 production in the hippocampus. These results demonstrate the importance of a multidisciplinary approach to future diet and microbiome studies, as diet not only impacts the gut microbiome composition but potentially systemic health as well.
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Affiliation(s)
- Viviana J. Mancilla
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Paige N. Braden-Kuhle
- Department of Psychology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA
| | - Kelly N. Brice
- Department of Psychology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA
| | - Allison E. Mann
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
- Department of Biological Sciences, College of Science, Clemson University, Clemson, SC 29634, USA
| | - Megan T. Williams
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Yan Zhang
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Michael J. Chumley
- Department of Biology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA;
| | - Robert C. Barber
- Department of Pharmacology and Neuroscience, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Sabrina N. White
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, USA
| | - Gary W. Boehm
- Department of Psychology, College of Science and Engineering, Texas Christian University, Fort Worth, TX 76109, USA
| | - Michael S. Allen
- Department of Microbiology, Immunology, and Genetics, School of Biomedical Sciences, University of North Texas Health Science Center, Fort Worth, TX 76107, 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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Vonaesch P, Billy V, Mann AE, Morien E, Habib A, Collard JM, Dédé M, Kapel N, Sansonetti PJ, Parfrey LW. The eukaryome of African children is influenced by geographic location, gut biogeography, and nutritional status. Microlife 2023; 4:uqad033. [PMID: 37680753 PMCID: PMC10481997 DOI: 10.1093/femsml/uqad033] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/17/2023] [Indexed: 09/09/2023]
Abstract
Eukaryotes have historically been studied as parasites, but recent evidence suggests they may be indicators of a healthy gut ecosystem. Here, we describe the eukaryome along the gastrointestinal tract of children aged 2-5 years and test for associations with clinical factors such as anaemia, intestinal inflammation, chronic undernutrition, and age. Children were enrolled from December 2016 to May 2018 in Bangui, Central African Republic and Antananarivo, Madagascar. We analyzed a total of 1104 samples representing 212 gastric, 187 duodenal, and 705 fecal samples using a metabarcoding approach targeting the full ITS2 region for fungi, and the V4 hypervariable region of the 18S rRNA gene for the overall eukaryome. Roughly, half of all fecal samples showed microeukaryotic reads. We find high intersubject variability, only a handful of taxa that are likely residents of the gastrointestinal tract, and frequent co-occurrence of eukaryotes within an individual. We also find that the eukaryome differs between the stomach, duodenum, and feces and is strongly influenced by country of origin. Our data show trends towards higher levels of Fusarium equiseti, a mycotoxin producing fungus, and lower levels of the protist Blastocystis in stunted children compared to nonstunted controls. Overall, the eukaryome is poorly correlated with clinical variables. Our study is of one of the largest cohorts analyzing the human intestinal eukaryome to date and the first to compare the eukaryome across different compartments of the gastrointestinal tract. Our results highlight the importance of studying populations across the world to uncover common features of the eukaryome in health.
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Affiliation(s)
- Pascale Vonaesch
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Vincent Billy
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Allison E Mann
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Evan Morien
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
| | - Azimdine Habib
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Jean-Marc Collard
- Unité de Bactériologie Expérimentale, Institut Pasteur de Madagascar, BP1274 Ambatofotsikely Avaradoha 101 Antananarivo, Madagascar
| | - Michel Dédé
- Laboratoire d’Analyse médicale, Institut Pasteur de Bangui, Avenue De Independence Bangui, 923 Central African Republic
| | - Nathalie Kapel
- Laboratoire de Coprologie Fonctionnelle, Assistance Publique- Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, 47-83 Bd de l’Hôpital, 75013 Paris, France
| | - Philippe J Sansonetti
- Unité de Pathogénie Microbienne Moléculaire, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Laura Wegener Parfrey
- Departments of Botany and Zoology, and Biodiversity Research Centre, University of British Columbia, 3200-6270 University Boulevard, V6T1Z4 Vancouver, Canada
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Tarone AM, Mann AE, Zhang Y, Zascavage RR, Mitchell EA, Morales E, Rusch TW, Allen MS. The devil is in the details: Variable impacts of season, BMI, sampling site temperature, and presence of insects on the post-mortem microbiome. Front Microbiol 2022; 13:1064904. [PMID: 36569070 PMCID: PMC9768039 DOI: 10.3389/fmicb.2022.1064904] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Post-mortem microbial communities are increasingly investigated as proxy evidence for a variety of factors of interest in forensic science. The reported predictive power of the microbial community to determine aspects of the individual's post-mortem history (e.g., the post-mortem interval) varies substantially among published research. This observed variation is partially driven by the local environment or the individual themselves. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. Materials and methods In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. Results We found that season, temperature at the sampling site, BMI, and sex had a significant effect on the post-mortem microbiome, the presence of insects has a homogenizing influence on the total bacterial community, and that community consistency from repeat sampling decreases as the decomposition process progresses. Moreover, we demonstrate the importance of temperature at the site of sampling on the abundance of important diagnostic taxa. Conclusion The results of this study suggest that while the bacterial community or specific bacterial species may prove to be useful for forensic applications, a clearer understanding of the mechanisms underpinning microbial decomposition will greatly increase the utility of microbial evidence in forensic casework.
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Affiliation(s)
- Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Allison E. Mann
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States,Department of Biological Sciences, Clemson University, Clemson, SC, United States
| | - Yan Zhang
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Roxanne R. Zascavage
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Elizabeth A. Mitchell
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Edgar Morales
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Travis W. Rusch
- Department of Entomology, Texas A&M University, College Station, TX, United States,Center for Grain and Animal Health Research, USDA Agricultural Research Service, Manhattan, KS, United States
| | - Michael S. Allen
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States,*Correspondence: Michael S. Allen,
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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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Mann AE, Mitchell EA, Zhang Y, Curtis-Robles R, Thapa S, Hamer SA, Allen MS. Comparison of the Bacterial Gut Microbiome of North American Triatoma spp. With and Without Trypanosoma cruzi. Front Microbiol 2020; 11:364. [PMID: 32231645 PMCID: PMC7082358 DOI: 10.3389/fmicb.2020.00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 10/16/2019] [Accepted: 02/18/2020] [Indexed: 12/20/2022] Open
Abstract
Chagas disease, caused by the hemoflagellate protist Trypanosoma cruzi, affects nearly 6 million people worldwide, mainly in Latin America. Hematophagous triatomine insects (“kissing bugs”) are the primary vectors of T. cruzi throughout the Americas and feed on a variety of animals, including humans. Control of triatomines is central to the control of T. cruzi infection. Recent advances in mitigation of other insect-borne diseases via the manipulation of insect-associated bacteria as a way to halt or slow disease transmission has opened questions to the applicability of these methods to Chagas disease vectors. Few studies have examined the hindgut microbiome of triatomines found in North America. In the current study, two species of triatomines were collected across Texas, United States, screened for the presence of T. cruzi, and analyzed for the bacterial composition of their hindguts using a 16S rRNA gene-fragment metabarcoding approach. We compared diversity of microbial community profiles across 74 triatomine insects to address the hypothesis that the richness and abundance of bacterial groups differ by T. cruzi infection and strain type, blood meal engorgement status, insect species, sex, and collection location. The gut microbial community of individual triatomines was characterized by low intraindividual taxonomic diversity and high interindividual variation that was weakly predicted by triatomine species, and was not predicted by triatomine sex, collection location, T. cruzi infection status, or blood meal score. However, we did find bacterial groups enriched in T. cruzi-positive individuals, including Enterobacterales, and Petrimonas. Additionally, we detected Salmonella enterica subspecies diarizonae in three triatomine individuals; this species is commonly associated with reptiles and domesticated animals and is a pathogen of humans. These data suggest that Triatoma spp. in Texas have variable patterns of colonized and transient bacteria, and may aid in development of novel means to interfere with transmission of the Chagas disease parasite T. cruzi. Deeper understanding of the effects of parasite infection on diverse insect vector microbiomes may highlight disease transmission risk and facilitate discovery of possible intervention strategies for biological control of this emerging vector-borne disease of global health significance.
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Affiliation(s)
- Allison E Mann
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Elizabeth A Mitchell
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Yan Zhang
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Rachel Curtis-Robles
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Santosh Thapa
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States.,Texas Children's Microbiome Center, Texas Children's Hospital, Houston, TX, United States.,Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Sarah A Hamer
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Michael S Allen
- Tick-Borne Disease Research Laboratory, Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
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Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt BW, Sankaranarayanan K, Ozga AT, Hoogland M, Hofman CA, Salazar-García DC, Frohlich B, Milner GR, Stone AC, Aldenderfer M, Lewis CM, Hofman CL, Warinner C, Schroeder H. The efficacy of whole human genome capture on ancient dental calculus and dentin. Am J Phys Anthropol 2018; 168:496-509. [PMID: 30586168 PMCID: PMC6519167 DOI: 10.1002/ajpa.23763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/09/2018] [Accepted: 11/10/2018] [Indexed: 12/28/2022]
Abstract
Objectives Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing. Results Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four‐fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on‐target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum‐level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off‐target sequences in human genome‐enriched calculus libraries may still be useful for oral microbiome reconstruction. Discussion While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
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Affiliation(s)
| | | | - Allison E Mann
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma
| | - Andrew T Ozga
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute for Human Origins, Arizona State University, Tempe, Arizona.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Domingo C Salazar-García
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | | | - George R Milner
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute for Human Origins, Arizona State University, Tempe, Arizona.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, California
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Corinne L Hofman
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Christina Warinner
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hannes Schroeder
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar-García DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C. Erratum: Corrigendum: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep 2016; 6:27163. [PMID: 27254246 PMCID: PMC4890581 DOI: 10.1038/srep27163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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11
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Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar-García DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep 2015; 5:16498. [PMID: 26563586 PMCID: PMC4643231 DOI: 10.1038/srep16498] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/14/2015] [Indexed: 12/18/2022] Open
Abstract
To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
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Affiliation(s)
- Kirsten A Ziesemer
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Allison E Mann
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | | | - Hannes Schroeder
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands.,Center for Geogenetics, University of Copenhagen, Denmark
| | - Andrew T Ozga
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands
| | - Andrea Waters-Rist
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Domingo C Salazar-García
- Department of Anthropology, University of Cape Town, South Africa.,Departament de Prehistòria i Arqueologia, Universitat de València, Spain.,Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mark Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, USA
| | | | - Jessica Hendy
- Department of Archaeology, University of York, York, UK
| | - Darlene A Weston
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands.,Department of Anthropology, University of British Columbia, Vancouver, Canada
| | | | | | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Corinne Hofman
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
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Abstract
Health care professionals frequently fail to recognize and address the misuse and abuse of alcohol and drugs in the elderly. Estimates of alcohol abuse in the older adult population range from 4% to 20% in the community dwelling elderly and up to approximately 25% among hospitalized older adults (Adams & Cox, 1995; Adams & Kinney, 1995; Beresford et al., 1990). In addition, the present population of older adults consumes 2-3 times more psychoactive medications than younger age groups (Sheahan et al., 1995). The effects of alcohol and substance abuse in older adults are influenced by physical, developmental, and psychosocial changes that occur with aging. Identification of alcohol and substance abuse presents a challenge for health care providers as older adults often present with atypical symptoms. Accurate diagnosis allows for the initiation of interventions for both immediate and long-term treatment.
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Affiliation(s)
- K A Ondus
- Cleveland Clinic Foundation, Ohio, USA
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13
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Thompson HS, Davies ML, Holding FP, Fallon RE, Mann AE, O'Neill T, Roberts JS. Phase I safety and antigenicity of TA-GW: a recombinant HPV6 L2E7 vaccine for the treatment of genital warts. Vaccine 1999; 17:40-9. [PMID: 10078606 DOI: 10.1016/s0264-410x(98)00146-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.8] [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: 11/24/2022]
Abstract
A phase I double-blind, randomized, placebo-controlled study was carried out in healthy subjects to assess the safety and immunogenicity of TA-GW, a recombinant HPV6 L2E7 fusion protein vaccine for the treatment of genital warts. Forty-two healthy male volunteers were randomised to receive three intramuscular injections of either 0, 3, 30 or 300 microg of recombinant L2E7 adsorbed onto Alhydrogel. Two vaccination schedules were compared: weeks 0, 1 and 4 (accelerated schedule) and weeks 0, 4 and 8 (classical schedule). Subjects were monitored for adverse events throughout. Immunogenicity was assessed by measuring L2E7 specific in vitro T cell proliferative responses, production of IFNgamma and IL-5 and serum antibodies. Dose-dependent and long-lived T and B cell immune responses were elicited by TA-GW with both vaccination schedules. In conclusion, TA-GW is both safe, well-tolerated and immunogenic. The results allow the selection of the 300-microg vaccine formulation and accelerated vaccination schedule for phase II trials in patients with genital warts.
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Affiliation(s)
- H S Thompson
- Cantab Pharmaceuticals Research Ltd, Cambridge, UK
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14
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Thompson HS, Davies ML, Watts MJ, Mann AE, Holding FP, O'Neill T, Beech JT, Thompson SJ, Leesman GD, Ulrich JT. Enhanced immunogenicity of a recombinant genital warts vaccine adjuvanted with monophosphoryl lipid A. Vaccine 1998; 16:1993-9. [PMID: 9796056 DOI: 10.1016/s0264-410x(98)00088-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [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: 02/09/2023]
Abstract
The regression of genital warts is believed to be a T-cell-mediated immune effect. We have sought to enhance the immunogenicity of a therapeutic vaccine for the treatment of genital warts with the use of the adjuvant monophosphoryl lipid A (MPL-immunostimulant), a detoxified form of the lipopolysaccharide (LPS) of Salmonella minnesota R595. The comparative immunogenicity and reactogenicity of a recombinant human papillomavirus type 6 (HPV6) L2E7 fusion protein in either aqueous, oil-in-water emulsions or Alhydrogel formulations containing MPL was evaluated. We conclude that the simple addition of MPL to the L2E7 fusion protein already adsorbed onto Alhydrogel preferentially enhances antigen specific in vitro T-cell proliferative responses, IFN gamma production and in vivo delayed type hypersensitivity responses without increasing its reactogenicity.
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Affiliation(s)
- H S Thompson
- Cantab Pharmaceuticals Research Ltd, Cambridge, UK
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15
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Abstract
Several recent studies have concluded that early hominines resembled apes in patterns of dental ontogeny and have inferred from this conclusion that they were ape-like in other aspects of growth and development as well. Prior to their employment on fossil juveniles, the comparative methods used in these studies were not first tested for their predictive accuracy in distinguishing modern humans from apes on the basis of proposed patterns of dental ontogeny. We find that 92% of a sample of 48 modern children are classified as ape-like or nonhuman by the criteria employed in one of these studies and overlap entirely with fossil juvenile dental patterns. The use of these methods to characterize early hominines as "ape-like" or distinctly divergent from humans is thus shown to be unwarranted.
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Affiliation(s)
- M Lampl
- Department of Anthropology, University of Pennsylvania, Philadelphia 19104
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16
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