The goal of BRCore is to aid the analysis of the Inter BRC Microbiome project by providing a set of tools to process and analyze microbial data from Bioenergy Research Centers. This is still an experimental package.
Install the development version of BRCore from GitHub with:
# install.packages("pak")
pak::pak("germs-lab/BRCore")
#> ℹ Loading metadata database✔ Loading metadata database ... done
#>
#> → Will install 1 package.
#> → The package (0 B) is cached.
#> + BRCore 0.0.0.9000 [bld][cmp] (GitHub: 1ad972a)
#> ℹ No downloads are needed, 1 pkg is cached
#> ✔ Got BRCore 0.0.0.9000 (source) (587.62 kB)
#> ℹ Packaging BRCore 0.0.0.9000
#> ✔ Packaged BRCore 0.0.0.9000 (475ms)
#> ℹ Building BRCore 0.0.0.9000
#> ✔ Built BRCore 0.0.0.9000 (9.5s)
#> ✔ Installed BRCore 0.0.0.9000 (github::germs-lab/BRCore@1ad972a) (25ms)
#> ✔ 1 pkg + 114 deps: kept 101, added 1, dld 1 (NA B) [15.8s]
library(phyloseq)
library(BRCore)
# Load the esophagus dataset
data(esophagus, package = "phyloseq")# Get the taxa names from the esophagus dataset
taxa_names <- taxa_names(esophagus)
# Define realistic taxonomy levels
kingdoms <- c("Bacteria", "Archaea")
phyla <- c(
"Firmicutes",
"Bacteroidetes",
"Proteobacteria",
"Actinobacteria",
"Euryarchaeota"
)
classes <- c(
"Clostridia",
"Bacteroidia",
"Gammaproteobacteria",
"Actinobacteria",
"Methanobacteria"
)
orders <- c(
"Clostridiales",
"Bacteroidales",
"Enterobacterales",
"Bifidobacteriales",
"Methanobacteriales"
)
families <- c(
"Lachnospiraceae",
"Bacteroidaceae",
"Enterobacteriaceae",
"Bifidobacteriaceae",
"Methanobacteriaceae"
)
genera <- c("Blautia",
"Bacteroides",
"Escherichia",
"Bifidobacterium",
"Methanobrevibacter")
species <- c(
"Blautia producta",
"Bacteroides fragilis",
"Escherichia coli",
"Bifidobacterium longum",
"Methanobrevibacter smithii"
)
# Create a mock taxonomy table
set.seed(8998); mock_taxonomy_table <- matrix(
c(
sample(kingdoms, length(taxa_names), replace = TRUE),
sample(phyla, length(taxa_names), replace = TRUE),
sample(classes, length(taxa_names), replace = TRUE),
sample(orders, length(taxa_names), replace = TRUE),
sample(families, length(taxa_names), replace = TRUE),
sample(genera, length(taxa_names), replace = TRUE),
sample(species, length(taxa_names), replace = TRUE)
),
nrow = length(taxa_names),
ncol = 7,
dimnames = list(
taxa_names,
c(
"Kingdom",
"Phylum",
"Class",
"Order",
"Family",
"Genus",
"Species"
)
)
)
# Convert to a taxonomy table object
tax_table <- tax_table(mock_taxonomy_table)
# Add sample metadata to the esophagus dataset
sample_data <- data.frame(
Sample = sample_names(esophagus),
Group = sample(c("A", "B"), nsamples(esophagus), replace = TRUE), # Random groups
row.names = sample_names(esophagus)
)
# Add the taxonomy table and sample metadata to the esophagus dataset
esophagus_with_tax <- merge_phyloseq(esophagus, tax_table, sample_data(sample_data))# Extract core microbial taxa
core_result <- extract_core(
physeq = esophagus_with_tax,
Var = "Group", # Variable in sample metadata to group by
method = "increase", # Method for core taxa selection
increase_value = 2 # Threshold for core taxa inclusion (2% contribution to Bray-Curtis dissimilarity)
)
#> ✔ Input phyloseq object is valid!
#> ℹ Calculating BC dissimilarity based on the 1st ranked OTU
#> ✔ BC dissimilarity based on the 1st ranked OTU complete
#> ℹ Calculating BC dissimilarity based on ranked OTUs, starting at 2025-03-26 11:12:55.287585
#> ✔ BC ranks done!
#> ✔ Performing method 'increase'
# View the results
print(core_result)
#> $core_otus
#> [1] "65_7_12" "65_2_17" "65_7_4" "59_5_2" "65_2_5" "59_7_6" "59_9_31"
#> [8] "59_5_19" "59_2_6" "65_6_2" "65_3_18" "59_9_17" "59_8_12" "59_4_25"
#> [15] "59_3_21"
#>
#> $bray_curtis_ranked
#> # A tibble: 44 × 4
#> rank MeanBC proportionBC IncreaseBC
#> <fct> <dbl> <dbl> <dbl>
#> 1 2 0.0985 0.186 1.15
#> 2 3 0.108 0.204 1.1
#> 3 4 0.117 0.220 1.08
#> 4 5 0.128 0.241 1.10
#> 5 6 0.133 0.251 1.04
#> 6 7 0.169 0.319 1.27
#> 7 8 0.181 0.341 1.07
#> 8 9 0.213 0.402 1.18
#> 9 10 0.351 0.663 1.65
#> 10 11 0.363 0.684 1.03
#> # ℹ 34 more rows
#>
#> $otu_rankings
#> otu rank
#> 1 59_8_22 1.0000000
#> 2 65_7_12 1.0000000
#> 3 65_2_17 1.0000000
#> 4 65_7_4 1.0000000
#> 5 59_5_2 1.0000000
#> 6 65_2_5 1.0000000
#> 7 59_7_6 1.0000000
#> 8 59_9_31 1.0000000
#> 9 59_5_19 1.0000000
#> 10 59_2_6 1.0000000
#> 11 65_6_2 0.3333333
#> 12 9_7_25 0.3333333
#> 13 65_9_13 0.3333333
#> 14 65_3_18 0.3333333
#> 15 59_9_17 0.3333333
#> 16 9_4_6 0.3333333
#> 17 59_5_13 0.1666667
#> 18 59_8_12 0.1666667
#> 19 65_3_22 0.1666667
#> 20 65_5_1 0.1666667
#> 21 65_1_10 0.1666667
#> 22 59_6_1 0.1666667
#> 23 65_9_26 0.1666667
#> 24 65_5_18 0.1666667
#> 25 65_8_12 0.1666667
#> 26 65_9_1 0.1666667
#> 27 59_9_26 0.1666667
#> 28 9_6_28 0.1666667
#> 29 65_4_26 0.1666667
#> 30 65_1_17 0.1666667
#> 31 9_4_3 0.1666667
#> 32 65_8_7 0.1666667
#> 33 59_4_5 0.1666667
#> 34 65_4_10 0.1666667
#> 35 9_4_5 0.1666667
#> 36 65_1_8 0.1666667
#> 37 9_4_13 0.1666667
#> 38 9_6_3 0.1666667
#> 39 59_9_18 0.1666667
#> 40 65_8_25 0.1666667
#> 41 65_8_29 0.1666667
#> 42 65_4_20 0.1666667
#> 43 59_4_25 0.1666667
#> 44 59_3_21 0.1666667
#> 45 59_4_16 0.1666667
#> 46 59_8_3 0.1666667
#> 47 65_9_9 0.1666667
#>
#> $occupancy_abundance
#> otu otu_occ otu_rel fill
#> 1 59_8_22 1.0000000 0.121510673 no
#> 2 59_5_13 0.3333333 0.001642036 no
#> 3 59_8_12 0.3333333 0.018062397 core
#> 4 65_3_22 0.3333333 0.001642036 no
#> 5 65_5_1 0.3333333 0.001642036 no
#> 6 65_1_10 0.3333333 0.001642036 no
#> 7 65_7_12 1.0000000 0.027914614 core
#> 8 59_6_1 0.3333333 0.001642036 no
#> 9 65_2_17 1.0000000 0.019704433 core
#> 10 65_9_26 0.3333333 0.008210181 no
#> 11 65_5_18 0.3333333 0.001642036 no
#> 12 65_8_12 0.3333333 0.001642036 no
#> 13 65_9_1 0.3333333 0.003284072 no
#> 14 59_9_26 0.3333333 0.006568144 no
#> 15 9_6_28 0.3333333 0.001642036 no
#> 16 65_7_4 1.0000000 0.014778325 core
#> 17 65_4_26 0.3333333 0.001642036 no
#> 18 65_1_17 0.3333333 0.004926108 no
#> 19 9_4_3 0.3333333 0.001642036 no
#> 20 65_8_7 0.3333333 0.003284072 no
#> 21 59_4_5 0.3333333 0.001642036 no
#> 22 59_5_2 1.0000000 0.021346470 core
#> 23 65_6_2 0.6666667 0.018062397 core
#> 24 65_4_10 0.3333333 0.004926108 no
#> 25 9_7_25 0.6666667 0.006568144 no
#> 26 9_4_5 0.3333333 0.006568144 no
#> 27 65_1_8 0.3333333 0.001642036 no
#> 28 65_2_5 1.0000000 0.009852217 core
#> 29 59_7_6 1.0000000 0.151067323 core
#> 30 59_9_31 1.0000000 0.026272578 core
#> 31 9_4_13 0.3333333 0.001642036 no
#> 32 9_6_3 0.3333333 0.003284072 no
#> 33 59_9_18 0.3333333 0.004926108 no
#> 34 65_9_13 0.6666667 0.008210181 no
#> 35 65_3_18 0.6666667 0.013136289 core
#> 36 65_8_25 0.3333333 0.004926108 no
#> 37 65_8_29 0.3333333 0.001642036 no
#> 38 65_4_20 0.3333333 0.004926108 no
#> 39 59_9_17 0.6666667 0.013136289 core
#> 40 9_4_6 0.6666667 0.008210181 no
#> 41 59_4_25 0.3333333 0.011494253 core
#> 42 59_3_21 0.3333333 0.013136289 core
#> 43 59_4_16 0.3333333 0.001642036 no
#> 44 59_8_3 0.3333333 0.004926108 no
#> 45 59_5_19 1.0000000 0.073891626 core
#> 46 65_9_9 0.3333333 0.001642036 no
#> 47 59_2_6 1.0000000 0.336617406 core
#>
#> $otu_table
#> B C D
#> 59_8_22 55 16 3
#> 59_5_13 0 1 0
#> 59_8_12 0 11 0
#> 65_3_22 0 1 0
#> 65_5_1 0 0 1
#> 65_1_10 0 0 1
#> 65_7_12 5 2 10
#> 59_6_1 0 1 0
#> 65_2_17 7 1 4
#> 65_9_26 0 0 5
#> 65_5_18 0 0 1
#> 65_8_12 0 0 1
#> 65_9_1 0 0 2
#> 59_9_26 0 4 0
#> 9_6_28 1 0 0
#> 65_7_4 1 6 2
#> 65_4_26 0 0 1
#> 65_1_17 0 3 0
#> 9_4_3 1 0 0
#> 65_8_7 2 0 0
#> 59_4_5 0 1 0
#> 59_5_2 2 9 2
#> 65_6_2 0 7 4
#> 65_4_10 0 3 0
#> 9_7_25 1 0 3
#> 9_4_5 4 0 0
#> 65_1_8 0 1 0
#> 65_2_5 1 4 1
#> 59_7_6 39 36 17
#> 59_9_31 7 8 1
#> 9_4_13 1 0 0
#> 9_6_3 2 0 0
#> 59_9_18 3 0 0
#> 65_9_13 0 1 4
#> 65_3_18 2 6 0
#> 65_8_25 0 0 3
#> 65_8_29 0 0 1
#> 65_4_20 0 0 3
#> 59_9_17 1 0 7
#> 9_4_6 0 3 2
#> 59_4_25 0 7 0
#> 59_3_21 0 8 0
#> 59_4_16 0 1 0
#> 59_8_3 0 3 0
#> 59_5_19 15 25 5
#> 65_9_9 0 0 1
#> 59_2_6 53 34 118
#>
#> $sample_metadata
#> Sample Group SampleID
#> B B A B
#> C C B C
#> C C A C
#>
#> $taxonomy_table
#> Kingdom Phylum Class Order
#> 59_8_22 Archaea Euryarchaeota Bacteroidia Methanobacteriales
#> 59_5_13 Bacteria Proteobacteria Gammaproteobacteria Bacteroidales
#> 59_8_12 Archaea Euryarchaeota Methanobacteria Clostridiales
#> 65_3_22 Bacteria Firmicutes Gammaproteobacteria Methanobacteriales
#> 65_5_1 Archaea Firmicutes Actinobacteria Clostridiales
#> 65_1_10 Archaea Actinobacteria Clostridia Enterobacterales
#> 65_7_12 Bacteria Bacteroidetes Methanobacteria Bifidobacteriales
#> 59_6_1 Archaea Firmicutes Methanobacteria Bacteroidales
#> 65_2_17 Bacteria Actinobacteria Bacteroidia Bifidobacteriales
#> 65_9_26 Archaea Firmicutes Actinobacteria Methanobacteriales
#> 65_5_18 Archaea Actinobacteria Clostridia Bacteroidales
#> 65_8_12 Bacteria Firmicutes Methanobacteria Enterobacterales
#> 65_9_1 Archaea Bacteroidetes Bacteroidia Methanobacteriales
#> 59_9_26 Bacteria Actinobacteria Gammaproteobacteria Methanobacteriales
#> 9_6_28 Archaea Proteobacteria Clostridia Bacteroidales
#> 65_7_4 Archaea Proteobacteria Gammaproteobacteria Clostridiales
#> 65_4_26 Archaea Bacteroidetes Methanobacteria Methanobacteriales
#> 65_1_17 Archaea Euryarchaeota Gammaproteobacteria Enterobacterales
#> 9_4_3 Archaea Euryarchaeota Methanobacteria Bacteroidales
#> 65_8_7 Bacteria Firmicutes Bacteroidia Bacteroidales
#> 59_4_5 Archaea Actinobacteria Bacteroidia Bacteroidales
#> 59_5_2 Archaea Actinobacteria Clostridia Enterobacterales
#> 65_6_2 Archaea Bacteroidetes Actinobacteria Bacteroidales
#> 65_4_10 Archaea Proteobacteria Clostridia Methanobacteriales
#> 9_7_25 Bacteria Bacteroidetes Actinobacteria Bifidobacteriales
#> 9_4_5 Bacteria Bacteroidetes Methanobacteria Clostridiales
#> 65_1_8 Bacteria Actinobacteria Actinobacteria Clostridiales
#> 65_2_5 Archaea Actinobacteria Clostridia Bifidobacteriales
#> 59_7_6 Bacteria Proteobacteria Gammaproteobacteria Enterobacterales
#> 59_9_31 Archaea Euryarchaeota Gammaproteobacteria Enterobacterales
#> 9_4_13 Bacteria Actinobacteria Actinobacteria Methanobacteriales
#> 9_6_3 Archaea Bacteroidetes Clostridia Bifidobacteriales
#> 59_9_18 Archaea Proteobacteria Actinobacteria Methanobacteriales
#> 65_9_13 Bacteria Bacteroidetes Gammaproteobacteria Bacteroidales
#> 65_3_18 Archaea Proteobacteria Clostridia Methanobacteriales
#> 65_8_25 Archaea Firmicutes Actinobacteria Methanobacteriales
#> 65_8_29 Bacteria Euryarchaeota Gammaproteobacteria Clostridiales
#> 65_4_20 Bacteria Actinobacteria Methanobacteria Enterobacterales
#> 59_9_17 Bacteria Firmicutes Methanobacteria Bacteroidales
#> 9_4_6 Archaea Bacteroidetes Methanobacteria Bifidobacteriales
#> 59_4_25 Bacteria Firmicutes Gammaproteobacteria Clostridiales
#> 59_3_21 Bacteria Proteobacteria Gammaproteobacteria Clostridiales
#> 59_4_16 Bacteria Bacteroidetes Actinobacteria Bifidobacteriales
#> 59_8_3 Bacteria Firmicutes Clostridia Clostridiales
#> 59_5_19 Archaea Firmicutes Methanobacteria Methanobacteriales
#> 65_9_9 Archaea Euryarchaeota Actinobacteria Bacteroidales
#> 59_2_6 Bacteria Firmicutes Bacteroidia Clostridiales
#> Family Genus Species
#> 59_8_22 Bacteroidaceae Bifidobacterium Escherichia coli
#> 59_5_13 Bifidobacteriaceae Bacteroides Blautia producta
#> 59_8_12 Lachnospiraceae Escherichia Blautia producta
#> 65_3_22 Methanobacteriaceae Blautia Escherichia coli
#> 65_5_1 Methanobacteriaceae Methanobrevibacter Bifidobacterium longum
#> 65_1_10 Bifidobacteriaceae Methanobrevibacter Blautia producta
#> 65_7_12 Enterobacteriaceae Escherichia Methanobrevibacter smithii
#> 59_6_1 Bifidobacteriaceae Methanobrevibacter Blautia producta
#> 65_2_17 Enterobacteriaceae Methanobrevibacter Methanobrevibacter smithii
#> 65_9_26 Enterobacteriaceae Bacteroides Bacteroides fragilis
#> 65_5_18 Enterobacteriaceae Bacteroides Blautia producta
#> 65_8_12 Bacteroidaceae Blautia Methanobrevibacter smithii
#> 65_9_1 Methanobacteriaceae Methanobrevibacter Bacteroides fragilis
#> 59_9_26 Methanobacteriaceae Blautia Bifidobacterium longum
#> 9_6_28 Bifidobacteriaceae Methanobrevibacter Methanobrevibacter smithii
#> 65_7_4 Methanobacteriaceae Blautia Escherichia coli
#> 65_4_26 Lachnospiraceae Escherichia Escherichia coli
#> 65_1_17 Bacteroidaceae Blautia Bifidobacterium longum
#> 9_4_3 Bifidobacteriaceae Blautia Escherichia coli
#> 65_8_7 Bacteroidaceae Blautia Methanobrevibacter smithii
#> 59_4_5 Enterobacteriaceae Blautia Bifidobacterium longum
#> 59_5_2 Bacteroidaceae Escherichia Escherichia coli
#> 65_6_2 Enterobacteriaceae Methanobrevibacter Blautia producta
#> 65_4_10 Enterobacteriaceae Blautia Escherichia coli
#> 9_7_25 Enterobacteriaceae Methanobrevibacter Bifidobacterium longum
#> 9_4_5 Methanobacteriaceae Methanobrevibacter Methanobrevibacter smithii
#> 65_1_8 Bacteroidaceae Blautia Bacteroides fragilis
#> 65_2_5 Bacteroidaceae Methanobrevibacter Escherichia coli
#> 59_7_6 Enterobacteriaceae Escherichia Bifidobacterium longum
#> 59_9_31 Lachnospiraceae Escherichia Blautia producta
#> 9_4_13 Lachnospiraceae Bacteroides Blautia producta
#> 9_6_3 Bifidobacteriaceae Blautia Escherichia coli
#> 59_9_18 Bifidobacteriaceae Bacteroides Bifidobacterium longum
#> 65_9_13 Bacteroidaceae Blautia Escherichia coli
#> 65_3_18 Enterobacteriaceae Escherichia Methanobrevibacter smithii
#> 65_8_25 Bifidobacteriaceae Bacteroides Bacteroides fragilis
#> 65_8_29 Enterobacteriaceae Escherichia Methanobrevibacter smithii
#> 65_4_20 Methanobacteriaceae Bacteroides Escherichia coli
#> 59_9_17 Enterobacteriaceae Escherichia Methanobrevibacter smithii
#> 9_4_6 Bacteroidaceae Bacteroides Blautia producta
#> 59_4_25 Bifidobacteriaceae Escherichia Methanobrevibacter smithii
#> 59_3_21 Methanobacteriaceae Bacteroides Bifidobacterium longum
#> 59_4_16 Enterobacteriaceae Methanobrevibacter Methanobrevibacter smithii
#> 59_8_3 Lachnospiraceae Bacteroides Escherichia coli
#> 59_5_19 Methanobacteriaceae Escherichia Bacteroides fragilis
#> 65_9_9 Lachnospiraceae Bifidobacterium Blautia producta
#> 59_2_6 Enterobacteriaceae Blautia Escherichia coliThe extract_core() function returns a list containing the following
elements:
-
core_otus: A vector of core OTUs identified based on the specified threshold.
-
bray_curtis_ranked: A data frame of Bray-Curtis dissimilarity rankings.
-
otu_rankings: A data frame of OTU rankings based on occupancy and abundance.
-
occupancy_abundance: A data frame of occupancy and abundance values for each OTU.
-
otu_table: The OTU table used for analysis.
-
sample_metadata: The sample metadata used for analysis.
-
taxonomy_table: The taxonomy table used for analysis.