Heritable oral microbes and their importance in microbiome research for public health

Andres Gomez

doi:10.1016/j.chom.2022.03.005

Heritable oral microbes and their importance in microbiome research for public health

Andres Gomez

Animal Science

Research output: Contribution to journal › Comment/debate › peer-review

Abstract

In 2016, I made part of an effort to characterize oral microbial communities in twins with dental caries. Here, I revisit the results published by me and my colleagues in Cell Host & Microbe in 2017, which shed light on plaque biofilm bacteria influenced by host genotype and their role in oral disease.

Original language	English (US)
Pages (from-to)	439-443
Number of pages	5
Journal	Cell Host and Microbe
Volume	30
Issue number	4
DOIs	https://doi.org/10.1016/j.chom.2022.03.005
State	Published - Apr 13 2022

Bibliographical note

Funding Information:
I sincerely want to thank Dr. Karen Nelson at the JCVI and collaborators at The University of Adelaide and The University of Melbourne for allowing me to be part of this exciting project. Besides Josh Espinoza, Chris Dupont, and Derek Harkins, I also want to thank other members of the JCVI team whose work set the stage to make this project possible, particularly Sara K. Highlander, Marcus B. Jones, and Manny Torralba. I want to thank the wonderful mentors I’ve had in my career and whose input not only helped me develop ideas for this project, but for the work I continue doing at The University of Minnesota—particularly Ran Blekhman (University of Minnesota), Brian White, Paul Garber (University of Illinois, Urbana-Champaign), Karen Nelson (JCVI), Steven Leigh (University of Colorado, Boulder), Gloria Cadavid (Universidad Nacional, Medellin, Colombia), and Jerry Sims (UIUC, currently, New Mexico State). Their mentoring, support, and, more importantly, their example has been instrumental in defining my role as a researcher, educator, advisor, and the kind of scientist I aspire to be. I also want to thank my collaborators Dr. Klara Petrzelkova at the Czech Academy of Sciences and Dr. Jess Rothman at Hunter College New York; their continued support has allowed me expand the resolution of questions regarding host-microbe interactions in the context of ecology and evolution. Last, I want to thank all the scientists that have contributed to our understanding of the interactions between host genetics and the microbiome, especially those whose work I could not mention due to space constraints. The research in the publication discussed was supported by the National Institute of Dental and Craniofacial Research of the National Institutes of Health under award number R01DE019665 to Dr. Karen Nelson.

Funding Information:
Based on this body of work, it made sense to apply the ACE model to investigate heritable bacterial taxa in the oral cavity and their role in dental caries. Calculating heritability of specific oral bacterial taxa was not the original intent of this project, but given that we had a good sample size (485 monozygotic and dizygotic Australian twins, 5?11 years old) and that data on genetic determinants of oral microbes were still scant, I thought that mining for heritability signals in this dataset was a must, besides making this piece a more interesting contribution. I had never used the ACE model to calculate heritability of microbiome traits, so I contacted Julia Goodrich, through Ran Blekhman, to get some perspective on how this model could be applied to our dataset. Julia was extremely helpful and pointed us to great resources to start. In addition, JCVI has an incredible staff of data and genomic scientists, so Dr. Karen Nelson and I teamed up with Derek Harkins (computational biologist), Josh Espinoza (staff scientist), and Professor Chris Dupont at JCVI to plan the analytical procedures that would lead us to find heritable taxa in the supragingival plaque of this twin cohort. Along with Josh and Chris, we strengthened heritability calculations for specific oral plaque taxa using Falconer's formula. Thus, I was very confident in the analytical support we had to find heritable signals on the oral microbiome. Furthermore, the team at The University of Melbourne and The University of Adelaide?which included Jeff Craig and Richard Saffery (epigenetics), Pamela Leong, Michelle Bockmann, and Toby Hughes (oral biology and health)?provided a very strong support to elucidate how plaque taxa could be associated with patterns of health and disease along the life course, and in the context of heritability.I sincerely want to thank Dr. Karen Nelson at the JCVI and collaborators at The University of Adelaide and The University of Melbourne for allowing me to be part of this exciting project. Besides Josh Espinoza, Chris Dupont, and Derek Harkins, I also want to thank other members of the JCVI team whose work set the stage to make this project possible, particularly Sara K. Highlander, Marcus B. Jones, and Manny Torralba. I want to thank the wonderful mentors I've had in my career and whose input not only helped me develop ideas for this project, but for the work I continue doing at The University of Minnesota?particularly Ran Blekhman (University of Minnesota), Brian White, Paul Garber (University of Illinois, Urbana-Champaign), Karen Nelson (JCVI), Steven Leigh (University of Colorado, Boulder), Gloria Cadavid (Universidad Nacional, Medellin, Colombia), and Jerry Sims (UIUC, currently, New Mexico State). Their mentoring, support, and, more importantly, their example has been instrumental in defining my role as a researcher, educator, advisor, and the kind of scientist I aspire to be. I also want to thank my collaborators Dr. Klara Petrzelkova at the Czech Academy of Sciences and Dr. Jess Rothman at Hunter College New York; their continued support has allowed me expand the resolution of questions regarding host-microbe interactions in the context of ecology and evolution. Last, I want to thank all the scientists that have contributed to our understanding of the interactions between host genetics and the microbiome, especially those whose work I could not mention due to space constraints. The research in the publication discussed was supported by the National Institute of Dental and Craniofacial Research of the National Institutes of Health under award number R01DE019665 to Dr. Karen Nelson. The authors declare no competing interests.

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© 2022 Elsevier Inc.

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title = "Heritable oral microbes and their importance in microbiome research for public health",

abstract = "In 2016, I made part of an effort to characterize oral microbial communities in twins with dental caries. Here, I revisit the results published by me and my colleagues in Cell Host & Microbe in 2017, which shed light on plaque biofilm bacteria influenced by host genotype and their role in oral disease.",

author = "Andres Gomez",

note = "Funding Information: I sincerely want to thank Dr. Karen Nelson at the JCVI and collaborators at The University of Adelaide and The University of Melbourne for allowing me to be part of this exciting project. Besides Josh Espinoza, Chris Dupont, and Derek Harkins, I also want to thank other members of the JCVI team whose work set the stage to make this project possible, particularly Sara K. Highlander, Marcus B. Jones, and Manny Torralba. I want to thank the wonderful mentors I{\textquoteright}ve had in my career and whose input not only helped me develop ideas for this project, but for the work I continue doing at The University of Minnesota—particularly Ran Blekhman (University of Minnesota), Brian White, Paul Garber (University of Illinois, Urbana-Champaign), Karen Nelson (JCVI), Steven Leigh (University of Colorado, Boulder), Gloria Cadavid (Universidad Nacional, Medellin, Colombia), and Jerry Sims (UIUC, currently, New Mexico State). Their mentoring, support, and, more importantly, their example has been instrumental in defining my role as a researcher, educator, advisor, and the kind of scientist I aspire to be. I also want to thank my collaborators Dr. Klara Petrzelkova at the Czech Academy of Sciences and Dr. Jess Rothman at Hunter College New York; their continued support has allowed me expand the resolution of questions regarding host-microbe interactions in the context of ecology and evolution. Last, I want to thank all the scientists that have contributed to our understanding of the interactions between host genetics and the microbiome, especially those whose work I could not mention due to space constraints. The research in the publication discussed was supported by the National Institute of Dental and Craniofacial Research of the National Institutes of Health under award number R01DE019665 to Dr. Karen Nelson. Funding Information: Based on this body of work, it made sense to apply the ACE model to investigate heritable bacterial taxa in the oral cavity and their role in dental caries. Calculating heritability of specific oral bacterial taxa was not the original intent of this project, but given that we had a good sample size (485 monozygotic and dizygotic Australian twins, 5?11 years old) and that data on genetic determinants of oral microbes were still scant, I thought that mining for heritability signals in this dataset was a must, besides making this piece a more interesting contribution. I had never used the ACE model to calculate heritability of microbiome traits, so I contacted Julia Goodrich, through Ran Blekhman, to get some perspective on how this model could be applied to our dataset. Julia was extremely helpful and pointed us to great resources to start. In addition, JCVI has an incredible staff of data and genomic scientists, so Dr. Karen Nelson and I teamed up with Derek Harkins (computational biologist), Josh Espinoza (staff scientist), and Professor Chris Dupont at JCVI to plan the analytical procedures that would lead us to find heritable taxa in the supragingival plaque of this twin cohort. Along with Josh and Chris, we strengthened heritability calculations for specific oral plaque taxa using Falconer's formula. Thus, I was very confident in the analytical support we had to find heritable signals on the oral microbiome. Furthermore, the team at The University of Melbourne and The University of Adelaide?which included Jeff Craig and Richard Saffery (epigenetics), Pamela Leong, Michelle Bockmann, and Toby Hughes (oral biology and health)?provided a very strong support to elucidate how plaque taxa could be associated with patterns of health and disease along the life course, and in the context of heritability.I sincerely want to thank Dr. Karen Nelson at the JCVI and collaborators at The University of Adelaide and The University of Melbourne for allowing me to be part of this exciting project. Besides Josh Espinoza, Chris Dupont, and Derek Harkins, I also want to thank other members of the JCVI team whose work set the stage to make this project possible, particularly Sara K. Highlander, Marcus B. Jones, and Manny Torralba. I want to thank the wonderful mentors I've had in my career and whose input not only helped me develop ideas for this project, but for the work I continue doing at The University of Minnesota?particularly Ran Blekhman (University of Minnesota), Brian White, Paul Garber (University of Illinois, Urbana-Champaign), Karen Nelson (JCVI), Steven Leigh (University of Colorado, Boulder), Gloria Cadavid (Universidad Nacional, Medellin, Colombia), and Jerry Sims (UIUC, currently, New Mexico State). Their mentoring, support, and, more importantly, their example has been instrumental in defining my role as a researcher, educator, advisor, and the kind of scientist I aspire to be. I also want to thank my collaborators Dr. Klara Petrzelkova at the Czech Academy of Sciences and Dr. Jess Rothman at Hunter College New York; their continued support has allowed me expand the resolution of questions regarding host-microbe interactions in the context of ecology and evolution. Last, I want to thank all the scientists that have contributed to our understanding of the interactions between host genetics and the microbiome, especially those whose work I could not mention due to space constraints. The research in the publication discussed was supported by the National Institute of Dental and Craniofacial Research of the National Institutes of Health under award number R01DE019665 to Dr. Karen Nelson. The authors declare no competing interests. Publisher Copyright: {\textcopyright} 2022 Elsevier Inc.",

year = "2022",

month = apr,

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doi = "10.1016/j.chom.2022.03.005",

language = "English (US)",

volume = "30",

pages = "439--443",

journal = "Cell Host and Microbe",

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AU - Gomez, Andres

N1 - Funding Information: I sincerely want to thank Dr. Karen Nelson at the JCVI and collaborators at The University of Adelaide and The University of Melbourne for allowing me to be part of this exciting project. Besides Josh Espinoza, Chris Dupont, and Derek Harkins, I also want to thank other members of the JCVI team whose work set the stage to make this project possible, particularly Sara K. Highlander, Marcus B. Jones, and Manny Torralba. I want to thank the wonderful mentors I’ve had in my career and whose input not only helped me develop ideas for this project, but for the work I continue doing at The University of Minnesota—particularly Ran Blekhman (University of Minnesota), Brian White, Paul Garber (University of Illinois, Urbana-Champaign), Karen Nelson (JCVI), Steven Leigh (University of Colorado, Boulder), Gloria Cadavid (Universidad Nacional, Medellin, Colombia), and Jerry Sims (UIUC, currently, New Mexico State). Their mentoring, support, and, more importantly, their example has been instrumental in defining my role as a researcher, educator, advisor, and the kind of scientist I aspire to be. I also want to thank my collaborators Dr. Klara Petrzelkova at the Czech Academy of Sciences and Dr. Jess Rothman at Hunter College New York; their continued support has allowed me expand the resolution of questions regarding host-microbe interactions in the context of ecology and evolution. Last, I want to thank all the scientists that have contributed to our understanding of the interactions between host genetics and the microbiome, especially those whose work I could not mention due to space constraints. The research in the publication discussed was supported by the National Institute of Dental and Craniofacial Research of the National Institutes of Health under award number R01DE019665 to Dr. Karen Nelson. Funding Information: Based on this body of work, it made sense to apply the ACE model to investigate heritable bacterial taxa in the oral cavity and their role in dental caries. Calculating heritability of specific oral bacterial taxa was not the original intent of this project, but given that we had a good sample size (485 monozygotic and dizygotic Australian twins, 5?11 years old) and that data on genetic determinants of oral microbes were still scant, I thought that mining for heritability signals in this dataset was a must, besides making this piece a more interesting contribution. I had never used the ACE model to calculate heritability of microbiome traits, so I contacted Julia Goodrich, through Ran Blekhman, to get some perspective on how this model could be applied to our dataset. Julia was extremely helpful and pointed us to great resources to start. In addition, JCVI has an incredible staff of data and genomic scientists, so Dr. Karen Nelson and I teamed up with Derek Harkins (computational biologist), Josh Espinoza (staff scientist), and Professor Chris Dupont at JCVI to plan the analytical procedures that would lead us to find heritable taxa in the supragingival plaque of this twin cohort. Along with Josh and Chris, we strengthened heritability calculations for specific oral plaque taxa using Falconer's formula. Thus, I was very confident in the analytical support we had to find heritable signals on the oral microbiome. Furthermore, the team at The University of Melbourne and The University of Adelaide?which included Jeff Craig and Richard Saffery (epigenetics), Pamela Leong, Michelle Bockmann, and Toby Hughes (oral biology and health)?provided a very strong support to elucidate how plaque taxa could be associated with patterns of health and disease along the life course, and in the context of heritability.I sincerely want to thank Dr. Karen Nelson at the JCVI and collaborators at The University of Adelaide and The University of Melbourne for allowing me to be part of this exciting project. Besides Josh Espinoza, Chris Dupont, and Derek Harkins, I also want to thank other members of the JCVI team whose work set the stage to make this project possible, particularly Sara K. Highlander, Marcus B. Jones, and Manny Torralba. I want to thank the wonderful mentors I've had in my career and whose input not only helped me develop ideas for this project, but for the work I continue doing at The University of Minnesota?particularly Ran Blekhman (University of Minnesota), Brian White, Paul Garber (University of Illinois, Urbana-Champaign), Karen Nelson (JCVI), Steven Leigh (University of Colorado, Boulder), Gloria Cadavid (Universidad Nacional, Medellin, Colombia), and Jerry Sims (UIUC, currently, New Mexico State). Their mentoring, support, and, more importantly, their example has been instrumental in defining my role as a researcher, educator, advisor, and the kind of scientist I aspire to be. I also want to thank my collaborators Dr. Klara Petrzelkova at the Czech Academy of Sciences and Dr. Jess Rothman at Hunter College New York; their continued support has allowed me expand the resolution of questions regarding host-microbe interactions in the context of ecology and evolution. Last, I want to thank all the scientists that have contributed to our understanding of the interactions between host genetics and the microbiome, especially those whose work I could not mention due to space constraints. The research in the publication discussed was supported by the National Institute of Dental and Craniofacial Research of the National Institutes of Health under award number R01DE019665 to Dr. Karen Nelson. The authors declare no competing interests. Publisher Copyright: © 2022 Elsevier Inc.

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Heritable oral microbes and their importance in microbiome research for public health

Abstract

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