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03-article.qmd
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---
subtitle: Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus
citation:
type: report
container-title: "bioRxiv"
doi: "10.1101/2023.05.23.541904"
url: https://doi.org/10.1101/2023.05.23.541904
author:
- name: Bjørn Peare Bartholdy
orcid: 0000-0003-3985-1016
corresponding: true
affiliations:
- ref: leiden
- name: Irina M. Velsko
orcid: 0000-0001-9810-9917
affiliations:
- ref: mpi
- name: Shira Gur-Arieh
orcid: 0000-0003-2015-7817
affiliations:
- ref: haifa
- ref: mun
- name: Zandra Fagernäs
orcid: 0000-0003-2667-3556
affiliations:
- ref: mpi
- ref: globe
- name: Christina Warinner
orcid: 0000-0002-4528-5877
affiliations:
- ref: harv
- ref: mpi
- name: Amanda G. Henry
orcid: 0000-0002-2923-4199
affiliations:
- ref: leiden
affiliations:
- id: leiden
name: Leiden University
department: Faculty of Archaeology
city: Leiden
country: The Netherlands
- id: mpi
name: Max Planck Institute for Evolutionary Anthropology
department: Department of Archaeogenetics
city: Leipzig
country: Germany
- id: globe
name: University of Copenhagen
department: Globe Institute
city: Copenhagen
country: Denmark
- id: haifa
name: University of Haifa
department: The Leon Recanati Institute for Maritime Studies
city: Haifa
country: Israel
- id: mun
name: Ludwig Maximilian University
department: Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces
city: Munich
country: Germany
- id: harv
name: Department of Anthropology, Harvard University
department: Department of Anthropology
city: Cambridge, MA
country: USA
---
# Article 1 {#byoc-valid}
::: {.content-visible when-format="pdf"}
\footnotesize
**Co-authors and contributions:**
- Irina M. Velsko, Max Planck Institute for Evolutionary Anthropology
- Shira Gur-Arieh, University of Haifa, Ludwig Maximilian University
- Zandra Fagernäs, Max Planck Institute for Evolutionary Anthropology, University of Copenhagen
- Christina Warinner, Max Planck Institute for Evolutionary Anthropology, Harvard University
- Amanda G. Henry, Leiden University
<!-- generated with tenzing (https://rollercoaster.shinyapps.io/tenzing/) -->
Conceptualization: B.P.B., I.M.V., S.G.-A., and A.G.H. Data curation: B.P.B. Formal analysis: B.P.B., I.M.V., and S.G.-A. Funding acquisition: C.W. and A.G.H. Investigation: B.P.B., S.G.-A., and Z.F. Methodology: B.P.B., I.M.V., and S.G.-A. Resources: C.W. and A.G.H. Software: B.P.B. Supervision: C.W. and A.G.H. Visualization: B.P.B. and I.M.V. Writing - original draft: B.P.B., I.M.V., S.G.-A., Z.F., and A.G.H. Writing - review & editing: B.P.B., I.M.V., S.G.-A., Z.F., and A.G.H.
**Cite as:**
Bartholdy, B. P., Velsko, I. M., Gur-Arieh, S., Fagernäs, Z., Warinner, C., & Henry, A. G. (2023, May 30). Assessing the validity of a calcifying oral biofilm model as a suitable proxy for dental calculus. https://doi.org/10.1101/2023.05.23.541904
\normalsize
{{< pagebreak >}}
:::
::: {.content-visible when-format="html"}
{{< var article1.badges.status >}} {{< var article1.badges.version >}} {{< var article1.badges.doi >}} {{< var article1.badges.github >}}
::: {.callout-note icon="false"}
## Summary {-}
This chapter is an article that describes a protocol for the growth of a calcifying
oral biofilm model, or artificial dental calculus. We also make sure that the
artificial dental calculus is a good substitute for the real thing by determining
the bacterial and mineral makeup of our model calculus and compare it to natural
dental calculus, both archaeological and modern.
:::
:::
```{r}
#| label: setup-byoc-valid
library(dplyr)
library(tidyr)
library(ggplot2)
library(stringr)
library(patchwork)
library(forcats)
library(cowplot)
library(readr)
library(here)
knitr::opts_chunk$set(fig.path = "figures/byoc-valid-")
dna_metadata <- read_tsv(here("articles/byoc-valid/01-documentation/metadata.tsv"))
dna_analysis_metadata <- read_tsv(here("articles/byoc-valid/01-documentation/analysis-metadata.tsv"))
dna_experiment_metadata <- read_tsv(here("articles/byoc-valid/01-documentation/experiment-metadata.tsv"))
bac_properties <- read_tsv(here("articles/byoc-valid/01-documentation/species-properties.tsv"))
genus_oxytol <- read_tsv(here("articles/byoc-valid/01-documentation/genus-O2tolerance.tsv"))
otu_table <- read_tsv(here("articles/byoc-valid/05-results/post-decontam_taxatable.tsv"))
pca_loadings <- readr::read_tsv(here("articles/byoc-valid/05-results/all-pca-loadings.tsv"))
load(here("articles/byoc-valid/05-results/spca_byoc.rda"))
load(here("articles/byoc-valid/05-results/spca_species.rda"))
alpha_div <- read_tsv(here("articles/byoc-valid/05-results/alpha-diversity.tsv"))
byoc_logf_full <- read_tsv(here("articles/byoc-valid/05-results/byoc_logf-full.tsv"))
plaque_logf_full <- read_tsv(here("articles/byoc-valid/05-results/plaque_logf-full.tsv"))
clr_compar_long <- readr::read_tsv(here("articles/byoc-valid/05-results/clr-compar.tsv")) %>%
pivot_longer(-sample, values_to = "clr_count", names_to = "species")
clr_byoc_long <- readr::read_tsv(here("articles/byoc-valid/05-results/clr-byoc.tsv")) %>%
pivot_longer(-sample, values_to = "clr_count", names_to = "species")
source(here("articles/byoc-valid/02-scripts/99_setup-qmd.R"))
source(here("articles/byoc-valid/02-scripts/99_metagen-figures.R"))
#ftir_metadata <- read_tsv(here("01-documentation/ftir-metadata.tsv"))
ftir_metadata <- read_tsv(here("articles/byoc-valid/01-documentation/ftir-metadata.tsv"))
ftir_data_raw <- read_csv(here("articles/byoc-valid/05-results/ftir-data.csv"))
ftir_grind_data <- read_csv(here("articles/byoc-valid/05-results/grind-data_cleaned.csv"))
source(here("articles/byoc-valid/02-scripts/99_tables.R"))
#source(here("02-scripts/99_figures.R"))
source(here("articles/byoc-valid/02-scripts/99_ftir-figures.R"))
# upload names and versions of software used
software_versions <- readr::read_tsv(here("articles/byoc-valid/01-documentation/software_versions.csv"), col_names = c("software", "version"))
```
## Introduction
{{< include articles/byoc-valid/07-publication/01-intro.qmd >}}
## Materials and methods
{{< include articles/byoc-valid/07-publication/02-matmet.qmd >}}
## Results
{{< include articles/byoc-valid/07-publication/03-results.qmd >}}
## Discussion
{{< include articles/byoc-valid/07-publication/04-disc.qmd >}}
## References cited