Exploring and preparing microbiome data

Overview

Questions

• How deeply was each sample sequenced?
• How do we look at the data at a higher taxonomic level, such as phylum?
• Why and how do we transform the counts?
• Which bacteria dominate the gut of the people in our study?

Objectives

• Plot the library sizes of the samples and explain why they matter.
• Agglomerate the data to a higher taxonomic rank.
• Transform counts into relative abundances and robust CLR (rclr) values, and explain what rclr does with the zeros.
• Plot the community composition of the samples and the abundance of a single taxon.
• Remove rare taxa with a prevalence filter.
• (Bonus) Store all taxonomic ranks in one object, and work with one rank using altExp() and swapAltExp().

Where are we?

---

We have our data in a TreeSE. Before we can answer our research question, we need to process the data: check its quality, summarize it and transform it. We also take a first look at which bacteria are in the samples.

Load packages and data

---

R

library(mia)
library(miaViz)

We load the TreeSE that we saved in the previous episode.

R

tse <- readRDS(file.path("data", "tse.rds"))

Library size

---

In episode 1, we learned that the total number of reads per sample, the library size, depends on the sequencing and not on the biology. Let’s check how much it varies. We sum the counts of each sample (column) and store the result as a new column in colData:

R

tse$library_size <- colSums(assay(tse, "counts"))
summary(tse$library_size)

OUTPUT

    Min.  1st Qu.   Median     Mean  3rd Qu.     Max.
 3283981  6947241  8709694  9222329 10478061 27686725 

The miaViz function plotHistogram() shows the distribution. With binwidth, we set the width of each bar, here one million reads:

R

plotHistogram(tse, col.var = "library_size", binwidth = 1e6)

Result: the largest sample has about 8 times more reads than the smallest. If we compared raw counts, the samples with more reads would seem to have more of everything. We fix this with a transformation below.

Agglomeration: moving up the tree of life

---

Our data is at the species level. Sometimes it is easier to look at bigger groups, such as genera or phyla. Combining all taxa that belong to the same group is called agglomeration. The counts of the taxa in a group are summed.

R

tse_phylum <- agglomerateByRank(tse, rank = "phylum")
rownames(tse_phylum)

OUTPUT

 [1] "Actinobacteria"             "Bacteroidota"
 [3] "Candidatus Melainabacteria" "Euryarchaeota"
 [5] "Firmicutes"                 "Fusobacteria"
 [7] "Lentisphaerae"              "Proteobacteria"
 [9] "Spirochaetes"               "Synergistetes"
[11] "Verrucomicrobia"           

Result: the 308 species belong to 11 phyla.

Challenge

Challenge 1: How many genera?

1. Agglomerate the data to the genus level and save the result as tse_genus.
2. How many genera are in the data?

Show me the solution

R

tse_genus <- agglomerateByRank(tse, rank = "genus")
nrow(tse_genus)

OUTPUT

[1] 104

Relative abundance

---

To compare samples with different library sizes, we transform the counts. The simplest transformation is the relative abundance: each count is divided by the library size of its sample. The result is the share of each taxon in the sample. For example, a taxon with 500 reads in a sample of 1000 reads has a relative abundance of 0.5 (50 %).

The function transformAssay() adds a transformed table to the TreeSE:

R

tse <- transformAssay(tse, assay.type = "counts", method = "relabundance")
assayNames(tse)

OUTPUT

[1] "counts"       "relabundance"

The TreeSE now holds two tables: the original counts and the new relabundance table. The original counts are kept.

Challenge

Challenge 2: Relative abundances

1. What do you expect the relative abundances of each sample (column) to sum to?
2. Check your answer for the first five samples.

Hint: colSums() sums the columns of a table.

Show me the solution

1. They sum to 1, because each value is the share of one taxon in the sample.
2. Check with colSums():

R

colSums(assay(tse, "relabundance"))[1:5]

OUTPUT

GupDM_A_11 GupDM_A_15   GupDM_A1  GupDM_A10  GupDM_A12
         1          1          1          1          1 

Community composition

---

Which bacteria dominate the gut of the people in our study? The miaViz function plotAbundance() draws a stacked bar for each sample. With group = "phylum", the taxa are agglomerated to phyla for the plot, and col.var = "disease" together with facet.cols = TRUE splits the samples into one panel per disease group. scales = "free_x" lets each panel show only its own samples.

R

plotAbundance(
    tse, assay.type = "relabundance", group = "phylum",
    col.var = "disease", facet.cols = TRUE, scales = "free_x"
)

WARNING

Warning: Removed 355 rows containing missing values or values outside the scale range
(`geom_bar()`).

Result: each bar is one person. Bacteroidota dominate most samples in both groups, followed by Firmicutes, but the communities vary a lot between people. Our eyes cannot tell from this plot whether the two groups differ. The analyses in the next episodes can.

Challenge

Challenge 3: The most abundant genera

Which five genera are the most abundant in the data?

Hint: use tse_genus from challenge 1 and the function getTop().

Show me the solution

R

getTop(tse_genus, top = 5)

OUTPUT

[1] "Prevotella"      "Bacteroides"     "Phocaeicola"     "Escherichia"
[5] "Bifidobacterium"

getTop() ranks the taxa by their mean abundance across the samples (by default in the counts table). Prevotella is the most abundant genus.

A closer look at one species

---

The most abundant species in the data is Prevotella copri. The miaViz function plotBoxplot() shows its relative abundance in each group. With features, we choose the taxon to plot, and with x, the groups:

R

plotBoxplot(
    tse, assay.type = "relabundance",
    features = "species-Prevotella_copri", x = "disease"
)

Result: in healthy people, P. copri makes up a median of 47 % of the whole community, compared to 1 % in people with CRC. A single species dominates the gut of many healthy people in this study. Keep this species in mind: we will meet it again in every episode that follows.

Robust CLR transformation

---

Relative abundances are intuitive, but they have a catch that we met in episode 1: because the shares of a sample always sum to 1, an increase of one taxon makes all the others look smaller. Log-ratio transformations are designed for this kind of relative (compositional) data. A ratio compares two taxa in the same sample, so it does not change when the sample is sequenced more deeply. The logarithm makes the ratios symmetric: a taxon that is twice as abundant as another gets log(2) = 0.69, and one that is half as abundant gets log(1/2) = -0.69.

The centred log-ratio (CLR) compares each taxon to the “average” taxon of the same sample (the geometric mean), on a log scale:

• a positive value means that the taxon is more abundant than average in that sample;
• a negative value means that it is less abundant than average;
• zero means that it is exactly average.

The logarithm of zero is not defined, and 84 % of our table is zeros. The robust CLR (rclr) solves this in two steps. First, it calculates the average from the non-zero values only. Then it fills in the zeros with estimates based on the main patterns in the whole table (matrix completion). In the version we use, all values are replaced by these smoothed estimates. The rclr values therefore describe the broad patterns in the data well, but a single value is an estimate, not a measurement. This is why we use rclr for methods that look at the whole table, such as PCA in episode 7, and relative abundances to plot single taxa.

R

tse <- transformAssay(tse, assay.type = "counts", method = "rclr")
assayNames(tse)

OUTPUT

[1] "counts"       "relabundance" "rclr"        

The TreeSE now holds three tables: counts, relabundance and rclr.

Why transform at all? Many statistical methods, such as PCA and the t-test, work best when the values are roughly normally distributed. Let’s compare the distribution of all values in the counts and rclr tables:

R

plotHistogram(tse, assay.type = "counts", binwidth = 1e5)

R

plotHistogram(tse, assay.type = "rclr", binwidth = 0.25)

Result: the counts are mostly zeros with a long tail of very large values. The rclr values form a bell-shaped distribution around zero, which suits many statistical methods much better.

Challenge

Challenge 4: What happened to the zeros?

Compare the counts and the rclr values of the first three taxa in the first three samples:

R

assay(tse, "counts")[1:3, 1:3]

OUTPUT

                                      GupDM_A_11 GupDM_A_15 GupDM_A1
species-Escherichia_coli                 1632336    5666898  6814491
species-Alistipes_putredinis              964884          0   225222
species-Porphyromonas_asaccharolytica     463162          0    92810

R

assay(tse, "rclr")[1:3, 1:3]

OUTPUT

                                      GupDM_A_11 GupDM_A_15 GupDM_A1
species-Escherichia_coli               1.0405323  1.7524587 4.724694
species-Alistipes_putredinis           0.6682048  1.3053407 2.961278
species-Porphyromonas_asaccharolytica  0.2550027  0.4543376 1.192139

1. Is Escherichia coli more or less abundant than the average taxon in the first sample?
2. In the second sample, two taxa have a count of zero. Which rclr values did they get? Were these taxa measured in that sample?

Show me the solution

1. Its rclr value is 1.04. It is positive, so E. coli is more abundant than the average taxon in that sample.
2. They got the values 1.31 and 0.45, although the taxa were not detected in that sample. The rclr filled in the zeros with estimates based on the patterns in the whole table. Keep in mind that these values are estimates, not measurements.

Removing rare taxa

---

Many taxa are found in only a few samples. The share of samples in which a taxon is found is called its prevalence. For some analyses, such as differential abundance in episode 8, it is useful to remove rare taxa: they carry little information and add many tests.

The function subsetByPrevalent() keeps only taxa that are found in at least a given share of the samples. Here, a taxon must have a relative abundance of at least 0.1 % (detection = 0.001) in at least 10 % of the samples (prevalence = 0.1):

R

tse_prevalent <- subsetByPrevalent(
    tse, assay.type = "relabundance",
    detection = 0.001, prevalence = 0.1
)
dim(tse_prevalent)

OUTPUT

[1] 94 60

Result: only 94 of the 308 species remain.

Callout

Filter or not?

Rare taxa are part of the diversity of a community. For the diversity analyses in episodes 6 and 7, we therefore use all taxa. We use the filtered data only for differential abundance analysis in episode 8.

Challenge

Challenge 5: A stricter filter

1. How many species remain if a species must be found in at least 50 % of the samples?
2. What does this tell you about the gut microbiomes of the people in this study?

Show me the solution

R

tse_prevalent50 <- subsetByPrevalent(
    tse, assay.type = "relabundance",
    detection = 0.001, prevalence = 0.5
)
nrow(tse_prevalent50)

OUTPUT

[1] 13

1. Only 13 species are found in at least half of the people.
2. Most species are found in only a few people: every gut microbiome is different.

Save the object

---

We save the TreeSE, which now contains the library sizes and the transformed tables, for the next episodes.

R

saveRDS(tse, file.path("data", "tse_processed.rds"))

Callout

Which table for which analysis?

There is no fixed rule: the right table depends on the method and on its assumptions. Some common choices:

• Alpha diversity is usually calculated from counts or relative abundances.
• Composition plots and Bray–Curtis dissimilarity use relative abundances.
• PCA and other methods that expect roughly normal values use rclr (or CLR) values.
• Differential abundance methods differ: some use log-transformed relative abundances (as we do in episode 8), some CLR values, and some model the counts directly.

Always check what the method you use expects. Many more transformations are available; see the Transformation chapter of OMA.

Challenge

Challenge 6: Explore the data at family level (30 minutes)

In this exercise, you use what you learned in this episode to explore the data at the family level.

1. Check that the library sizes do not differ between the disease groups: plot library_size by disease with plotBoxplot() and test the difference with the Wilcoxon test, daa::getWilcoxonTest(tse, library_size ~ disease) (we explain this test in the next episode). Why is it good news if they do not differ?
2. Agglomerate the data to the family level with agglomerateByRank(), and add relative abundances with transformAssay().
3. Find the five most abundant families with getTop() (use the relabundance table).
4. Plot the relative abundance of these five families by disease with plotBoxplot().
5. Which family dominates the healthy samples? Which family is more abundant in CRC? Write two sentences on how this fits with what you learned about Prevotella copri.

Show me the solution

1. Library size

R

plotBoxplot(tse, col.var = "library_size", x = "disease")

R

library_test <- daa::getWilcoxonTest(tse, library_size ~ disease)
library_test

OUTPUT

# A tibble: 1 × 8
  rownames     .y.          group1 group2     n1    n2 statistic     p
* <chr>        <chr>        <chr>  <chr>   <int> <int>     <dbl> <dbl>
1 library_size library_size CRC    healthy    30    30       438 0.866

The library sizes do not differ between the groups (p = 0.87). This is good news: if one group had been sequenced much more deeply, differences between the groups could partly be caused by the sequencing.

2.–4. Family level

R

tse_family <- agglomerateByRank(tse, rank = "family")

WARNING

Warning: 'rclr' includes negative values.
Agglomeration of it might lead to meaningless values.
Check the assay, and consider doing transformation againmanually with agglomerated data.

R

tse_family <- transformAssay(
    tse_family, assay.type = "counts", method = "relabundance"
)
top_families <- getTop(tse_family, top = 5, assay.type = "relabundance")
top_families

OUTPUT

[1] "Prevotellaceae"     "Bacteroidaceae"     "Enterobacteriaceae"
[4] "Lachnospiraceae"    "Oscillospiraceae"  

R

plotBoxplot(
    tse_family, assay.type = "relabundance", x = "disease",
    features = top_families, facet.by = "rownames"
)

agglomerateByRank() warns that 'rclr' includes negative values. Agglomeration sums the values of all tables. Summed counts are fine, but summed rclr values are meaningless. The rule is: agglomerate first, then transform. This is why we calculated the relative abundances again after agglomerating.

5. Prevotellaceae dominate the healthy samples (median 63 % vs 32 % in CRC), while Bacteroidaceae are more abundant in CRC (median 18 % vs 2 %). Most of the Prevotellaceae in healthy people is Prevotella copri; in CRC, its place is partly taken by Bacteroides.

Bonus: all ranks in one object

---

This section is optional. It shows a way to keep the data at all taxonomic ranks in one object, which is handy in larger analyses. The next episodes do not need it.

So far, we created a separate object for each rank (tse_phylum, tse_genus, tse_family). With many ranks, this quickly becomes hard to manage: each object must be transformed, subset and saved on its own.

Instead, we can keep all ranks in one object. The function agglomerateByRanks() agglomerates the data to every taxonomic rank at once:

R

tse <- agglomerateByRanks(tse)
altExpNames(tse)

OUTPUT

[1] "superkingdom" "phylum"       "class"        "order"        "family"
[6] "genus"        "species"     

When you run this, R prints a warning for each rank (we hide them on this page): 'rclr' includes negative values. Agglomeration sums the values of all tables. Summed counts are fine, but summed rclr values are meaningless. The rule is: agglomerate first, then transform. We therefore transform the agglomerated data again below.

The main data is still the species-level data that we named "main" in episode 4. Each rank is stored inside the TreeSE as an alternative experiment (altExp): a complete TreeSE of its own, with the same samples. We pick one with altExp():

R

altExp(tse, "phylum")

OUTPUT

class: TreeSummarizedExperiment
dim: 11 60
metadata(1): agglomerated_by_rank
assays(3): counts relabundance rclr
rownames(11): Actinobacteria Bacteroidota ... Synergistetes
  Verrucomicrobia
rowData names(7): superkingdom phylum ... genus species
colnames(60): GupDM_A_11 GupDM_A_15 ... GupDM_JO GupDM_JP
colData names(28): study_name subject_id ... disease_location
  library_size
reducedDimNames(0):
mainExpName: main
altExpNames(0):
rowLinks: a LinkDataFrame (11 rows)
rowTree: 1 phylo tree(s) (11 leaves)
colLinks: NULL
colTree: NULL

With the altexp argument, transformAssay() transforms the main data and all the alternative experiments with a single command:

R

tse <- transformAssay(
    tse, assay.type = "counts", method = "relabundance",
    altexp = altExpNames(tse)
)
tse <- transformAssay(
    tse, assay.type = "counts", method = "rclr",
    altexp = altExpNames(tse)
)
assayNames(altExp(tse, "phylum"))

OUTPUT

[1] "counts"       "relabundance" "rclr"        

The table names are the same as before, but the meaningless summed relabundance and rclr tables have now been replaced by tables calculated from the agglomerated counts.

Most functions work on the main data of a TreeSE. To analyse another rank, we make it the main data with swapAltExp(). The family-level data already has the sample information, so withColData = FALSE tells the function not to copy it a second time from the old main data:

R

tse_family <- swapAltExp(tse, "family", withColData = FALSE)
tse_family

OUTPUT

class: TreeSummarizedExperiment
dim: 48 60
metadata(1): agglomerated_by_rank
assays(3): counts relabundance rclr
rownames(48): Acidaminococcaceae Actinomycetaceae ... Veillonellaceae
  Victivallaceae
rowData names(7): superkingdom phylum ... genus species
colnames(60): GupDM_A_11 GupDM_A_15 ... GupDM_JO GupDM_JP
colData names(28): study_name subject_id ... disease_location
  library_size
reducedDimNames(0):
mainExpName: family
altExpNames(7): superkingdom phylum ... species main
rowLinks: a LinkDataFrame (48 rows)
rowTree: 1 phylo tree(s) (48 leaves)
colLinks: NULL
colTree: NULL

tse_family has families as its rows (mainExpName: family), and its other ranks, including the original "main" data, are still available as alternative experiments.

Callout

Why alternative experiments?

Alternative experiments are harder to understand than separate objects, but they have big advantages: all ranks share the same sample information, they stay in sync when we subset samples, one command transforms all of them, and we save a single object.

Challenge

Challenge 7 (bonus): Working at the genus level

1. Use swapAltExp() to make the genus level the main data. Store the result in tse_genus.
2. Which tables (assays) does it have?
3. Find the five most abundant genera with getTop(). Do you get the same answer as in challenge 3?

Show me the solution

R

tse_genus <- swapAltExp(tse, "genus", withColData = FALSE)
assayNames(tse_genus)

OUTPUT

[1] "counts"       "relabundance" "rclr"        

R

getTop(tse_genus, top = 5)

OUTPUT

[1] "Prevotella"      "Bacteroides"     "Phocaeicola"     "Escherichia"
[5] "Bifidobacterium"

The genus-level data already has the relabundance and rclr tables, and the top genera are the same as in challenge 3.

Key Points

• Library sizes differ between samples, so we compare relative values instead of raw counts.
• agglomerateByRank() combines taxa into a higher taxonomic rank.
• (Bonus) agglomerateByRanks() stores the data at every rank as alternative experiments in one object; altExp() picks one, and swapAltExp() makes one the main data.
• transformAssay() adds transformed tables, such as relative abundance and robust CLR (rclr), and keeps the original counts.
• rclr compares each taxon to the average taxon of its sample on a log scale. It fills in the zeros with estimates, so single rclr values are estimates, not measurements.
• Which table to use depends on the method and its assumptions. The rclr values are closer to a normal distribution than the counts.
• plotAbundance() shows the community composition of each sample, and plotBoxplot() the abundance of a single taxon by group.
• subsetByPrevalent() removes rare taxa. Use it for differential abundance, but not for diversity.
• In our study, one species, Prevotella copri, dominates the gut of many healthy people.