Project FOMC4083_4106_4511_4917 services include NGS sequencing of the V1V3 region of the 16S rRNA amplicons from the samples. First and foremost, please
download this report, as well as the sequence raw data from the download links provided below.
These links will expire after 60 days. We cannot guarantee the availability of your data after 60 days.
Full Bioinformatics analysis service was requested. We provide many analyses, starting from the raw sequence quality and noise filtering, pair reads merging, as well as chimera filtering for the sequences, using the
DADA2 denosing algorithm and pipeline.
We also provide many downstream analyses such as taxonomy assignment, alpha and beta diversity analyses, and differential abundance analysis.
For taxonomy assignment, most informative would be the taxonomy barplots. We provide an interactive barplots to show the relative abundance of microbes at different taxonomy levels (from Phylum to species) that you can choose.
If you specify which groups of samples you want to compare for differential abundance, we provide both ANCOM and LEfSe differential abundance analysis.
The samples were processed and analyzed with the ZymoBIOMICS® Service: Targeted
Metagenomic Sequencing (Zymo Research, Irvine, CA).
DNA Extraction: If DNA extraction was performed, one of three different DNA
extraction kits was used depending on the sample type and sample volume and were
used according to the manufacturer’s instructions, unless otherwise stated. The kit used
in this project is marked below:
☐
ZymoBIOMICS® DNA Miniprep Kit (Zymo Research, Irvine, CA)
☐
ZymoBIOMICS® DNA Microprep Kit (Zymo Research, Irvine, CA)
☐
ZymoBIOMICS®-96 MagBead DNA Kit (Zymo Research, Irvine, CA)
☑
N/A (DNA Extraction Not Performed)
Elution Volume: 50µL
Additional Notes: NA
Targeted Library Preparation: The DNA samples were prepared for targeted
sequencing with the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA).
These primers were custom designed by Zymo Research to provide the best coverage
of the 16S gene while maintaining high sensitivity. The primer sets used in this project
are marked below:
☐
Quick-16S™ Primer Set V1-V2 (Zymo Research, Irvine, CA)
☑
Quick-16S™ Primer Set V1-V3 (Zymo Research, Irvine, CA)
☐
Quick-16S™ Primer Set V3-V4 (Zymo Research, Irvine, CA)
☐
Quick-16S™ Primer Set V4 (Zymo Research, Irvine, CA)
☐
Quick-16S™ Primer Set V6-V8 (Zymo Research, Irvine, CA)
☐
Other: NA
Additional Notes: NA
The sequencing library was prepared using an innovative library preparation process in
which PCR reactions were performed in real-time PCR machines to control cycles and
therefore limit PCR chimera formation. The final PCR products were quantified with
qPCR fluorescence readings and pooled together based on equal molarity. The final
pooled library was cleaned up with the Select-a-Size DNA Clean & Concentrator™
(Zymo Research, Irvine, CA), then quantified with TapeStation® (Agilent Technologies,
Santa Clara, CA) and Qubit® (Thermo Fisher Scientific, Waltham, WA).
Control Samples: The ZymoBIOMICS® Microbial Community Standard (Zymo
Research, Irvine, CA) was used as a positive control for each DNA extraction, if
performed. The ZymoBIOMICS® Microbial Community DNA Standard (Zymo Research,
Irvine, CA) was used as a positive control for each targeted library preparation.
Negative controls (i.e. blank extraction control, blank library preparation control) were
included to assess the level of bioburden carried by the wet-lab process.
Sequencing: The final library was sequenced on Illumina® MiSeq™ with a V3 reagent kit
(600 cycles). The sequencing was performed with 10% PhiX spike-in.
The complete report of your project, including all links in this report, can be downloaded by clicking the link provided below. The downloaded file is a compressed ZIP file and once unzipped, open the file “REPORT.html” (may only shown as "REPORT" in your computer) by double clicking it. Your default web browser will open it and you will see the exact content of this report.
Please download and save the file to your computer storage device. The download link will expire after 60 days upon your receiving of this report.
Complete report download link:
To view the report, please follow the following steps:
1.
Download the .zip file from the report link above.
2.
Extract all the contents of the downloaded .zip file to your desktop.
3.
Open the extracted folder and find the "REPORT.html" (may shown as only "REPORT").
4.
Open (double-clicking) the REPORT.html file. Your default browser will open the top age of the complete report. Within the
report, there are links to view all the analyses performed for the project.
The raw NGS sequence data is available for download with the link provided below. The data is a compressed ZIP file and can be unzipped to individual sequence files.
Since this is a pair-end sequencing, each of your samples is represented by two sequence files, one for READ 1,
with the file extension “*_R1.fastq.gz”, another READ 2, with the file extension “*_R1.fastq.gz”.
The files are in FASTQ format and are compressed. FASTQ format is a text-based data format for storing both a biological sequence
and its corresponding quality scores. Most sequence analysis software will be able to open them.
The Sample IDs associated with the R1 and R2 fastq files are listed in the table below:
Sample ID
Original Sample ID
Read 1 File Name
Read 2 File Name
FOMC4083_4106_4511_4917.S01
zr4083_10V1V3_R1.fastq.gz
zr4083_10V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S02
zr4083_11V1V3_R1.fastq.gz
zr4083_11V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S03
zr4083_12V1V3_R1.fastq.gz
zr4083_12V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S04
zr4083_13V1V3_R1.fastq.gz
zr4083_13V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S05
zr4083_14V1V3_R1.fastq.gz
zr4083_14V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S06
zr4083_15V1V3_R1.fastq.gz
zr4083_15V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S07
zr4083_16V1V3_R1.fastq.gz
zr4083_16V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S08
zr4083_17V1V3_R1.fastq.gz
zr4083_17V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S09
zr4083_18V1V3_R1.fastq.gz
zr4083_18V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S10
zr4083_19V1V3_R1.fastq.gz
zr4083_19V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S11
zr4083_1V1V3_R1.fastq.gz
zr4083_1V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S12
zr4083_20V1V3_R1.fastq.gz
zr4083_20V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S13
zr4083_2V1V3_R1.fastq.gz
zr4083_2V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S14
zr4083_3V1V3_R1.fastq.gz
zr4083_3V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S15
zr4083_4V1V3_R1.fastq.gz
zr4083_4V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S16
zr4083_5V1V3_R1.fastq.gz
zr4083_5V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S17
zr4083_6V1V3_R1.fastq.gz
zr4083_6V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S18
zr4083_7V1V3_R1.fastq.gz
zr4083_7V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S19
zr4083_8V1V3_R1.fastq.gz
zr4083_8V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S20
zr4083_9V1V3_R1.fastq.gz
zr4083_9V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S21
zr4106_1V1V3_R1.fastq.gz
zr4106_1V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S22
zr4106_2V1V3_R1.fastq.gz
zr4106_2V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S23
zr4106_3V1V3_R1.fastq.gz
zr4106_3V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S24
zr4106_4V1V3_R1.fastq.gz
zr4106_4V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S25
zr4106_5V1V3_R1.fastq.gz
zr4106_5V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S26
zr4106_6V1V3_R1.fastq.gz
zr4106_6V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S27
zr4106_7V1V3_R1.fastq.gz
zr4106_7V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S28
zr4106_8V1V3_R1.fastq.gz
zr4106_8V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S29
zr4106_9V1V3_R1.fastq.gz
zr4106_9V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S30
zr4511_1V1V3_R1.fastq.gz
zr4511_1V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S31
zr4511_2V1V3_R1.fastq.gz
zr4511_2V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S32
zr4917_1V1V3_R1.fastq.gz
zr4917_1V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S33
zr4917_2V1V3_R1.fastq.gz
zr4917_2V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S34
zr4917_3V1V3_R1.fastq.gz
zr4917_3V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S35
zr4917_4V1V3_R1.fastq.gz
zr4917_4V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S36
zr4917_5V1V3_R1.fastq.gz
zr4917_5V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S37
zr4917_6V1V3_R1.fastq.gz
zr4917_6V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S38
zr4917_7V1V3_R1.fastq.gz
zr4917_7V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S39
zr4917_8V1V3_R1.fastq.gz
zr4917_8V1V3_R2.fastq.gz
FOMC4083_4106_4511_4917.S40
zr4917_9V1V3_R1.fastq.gz
zr4917_9V1V3_R2.fastq.gz
Please download and save the file to your computer storage device. The download link will expire after 60 days upon your receiving of this report.
DADA2 is a software package that models and corrects Illumina-sequenced amplicon errors.
DADA2 infers sample sequences exactly, without coarse-graining into OTUs,
and resolves differences of as little as one nucleotide. DADA2 identified more real variants
and output fewer spurious sequences than other methods.
DADA2’s advantage is that it uses more of the data. The DADA2 error model incorporates quality information,
which is ignored by all other methods after filtering. The DADA2 error model incorporates quantitative abundances,
whereas most other methods use abundance ranks if they use abundance at all.
The DADA2 error model identifies the differences between sequences, eg. A->C,
whereas other methods merely count the mismatches. DADA2 can parameterize its error model from the data itself,
rather than relying on previous datasets that may or may not reflect the PCR and sequencing protocols used in your study.
DADA2 pipeline includes several tools for read quality control, including quality filtering, trimming, denoising, pair merging and chimera filtering. Below are the major processing steps of DADA2:
Step 1. Read trimming based on sequence quality
The quality of NGS Illumina sequences often decreases toward the end of the reads.
DADA2 allows to trim off the poor quality read ends in order to improve the error
model building and pair mergicing performance.
Step 2. Learn the Error Rates
The DADA2 algorithm makes use of a parametric error model (err) and every
amplicon dataset has a different set of error rates. The learnErrors method
learns this error model from the data, by alternating estimation of the error
rates and inference of sample composition until they converge on a jointly
consistent solution. As in many machine-learning problems, the algorithm must
begin with an initial guess, for which the maximum possible error rates in
this data are used (the error rates if only the most abundant sequence is
correct and all the rest are errors).
Step 3. Infer amplicon sequence variants (ASVs) based on the error model built in previous step. This step is also called sequence "denoising".
The outcome of this step is a list of ASVs that are the equivalent of oligonucleotides.
Step 4. Merge paired reads. If the sequencing products are read pairs, DADA2 will merge the R1 and R2 ASVs into single sequences.
Merging is performed by aligning the denoised forward reads with the reverse-complement of the corresponding
denoised reverse reads, and then constructing the merged “contig” sequences.
By default, merged sequences are only output if the forward and reverse reads overlap by
at least 12 bases, and are identical to each other in the overlap region (but these conditions can be changed via function arguments).
Step 5. Remove chimera.
The core dada method corrects substitution and indel errors, but chimeras remain. Fortunately, the accuracy of sequence variants
after denoising makes identifying chimeric ASVs simpler than when dealing with fuzzy OTUs.
Chimeric sequences are identified if they can be exactly reconstructed by
combining a left-segment and a right-segment from two more abundant “parent” sequences. The frequency of chimeric sequences varies substantially
from dataset to dataset, and depends on on factors including experimental procedures and sample complexity.
Results
1. Read Quality Plots NGS sequence analaysis starts with visualizing the quality of the sequencing. Below are the quality plots of the first
sample for the R1 and R2 reads separately. In gray-scale is a heat map of the frequency of each quality score at each base position. The mean
quality score at each position is shown by the green line, and the quartiles of the quality score distribution by the orange lines.
The forward reads are usually of better quality. It is a common practice to trim the last few nucleotides to avoid less well-controlled errors
that can arise there. The trimming affects the downstream steps including error model building, merging and chimera calling. FOMC uses an empirical
approach to test many combinations of different trim length in order to achieve best final amplicon sequence variants (ASVs), see the next
section “Optimal trim length for ASVs”.
Below is the link to a PDF file for viewing the quality plots for all samples:
2. Optimal trim length for ASVs The final number of merged and chimera-filtered ASVs depends on the quality filtering (hence trimming) in the very beginning of the DADA2 pipeline.
In order to achieve highest number of ASVs, an empirical approach was used -
Create a random subset of each sample consisting of 5,000 R1 and 5,000 R2 (to reduce computation time)
Trim 10 bases at a time from the ends of both R1 and R2 up to 50 bases
For each combination of trimmed length (e.g., 300x300, 300x290, 290x290 etc), the trimmed reads are
subject to the entire DADA2 pipeline for chimera-filtered merged ASVs
The combination with highest percentage of the input reads becoming final ASVs is selected for the complete set of data
Below is the result of such operation, showing ASV percentages of total reads for all trimming combinations (1st Column = R1 lengths in bases; 1st Row = R2 lengths in bases):
R1/R2
281
271
261
251
241
231
321
27.49%
38.42%
44.65%
45.96%
48.37%
44.33%
311
28.27%
40.15%
45.87%
47.53%
46.13%
29.09%
301
28.67%
40.16%
45.97%
43.27%
29.04%
11.99%
291
28.55%
39.56%
41.81%
27.38%
12.60%
11.43%
281
29.99%
36.71%
26.01%
11.57%
11.72%
9.20%
271
25.82%
23.96%
10.94%
10.56%
9.03%
3.48%
Based on the above result, the trim length combination of R1 = 321 bases and R2 = 241 bases (highlighted red above), was chosen for generating final ASVs for all sequences.
This combination generated highest number of merged non-chimeric ASVs and was used for downstream analyses, if requested.
3. Error plots from learning the error rates
After DADA2 building the error model for the set of data, it is always worthwhile, as a sanity check if nothing else, to visualize the estimated error rates.
The error rates for each possible transition (A→C, A→G, …) are shown below. Points are the observed error rates for each consensus quality score.
The black line shows the estimated error rates after convergence of the machine-learning algorithm.
The red line shows the error rates expected under the nominal definition of the Q-score.
The ideal result would be the estimated error rates (black line) are a good fit to the observed rates (points), and the error rates drop
with increased quality as expected.
Forward Read R1 Error Plot
Reverse Read R2 Error Plot
The PDF version of these plots are available here:
4. DADA2 Result Summary The table below shows the summary of the DADA2 analysis,
tracking paired read counts of each samples for all the steps during DADA2 denoising process -
including end-trimming (filtered), denoising (denoisedF, denoisedF), pair merging (merged) and chimera removal (nonchim).
Sample ID
F4083.S01
F4083.S02
F4083.S03
F4083.S04
F4083.S05
F4083.S06
F4083.S07
F4083.S08
F4083.S09
F4083.S10
F4083.S11
F4083.S12
F4083.S13
F4083.S14
F4083.S15
F4083.S16
F4083.S17
F4083.S18
F4083.S19
F4083.S20
F4106.S21
F4106.S22
F4106.S23
F4106.S24
F4106.S25
F4106.S26
F4106.S27
F4106.S28
F4106.S29
F4511.S30
F4511.S31
F4917.S32
F4917.S33
F4917.S34
F4917.S35
F4917.S36
F4917.S37
F4917.S38
F4917.S39
F4917.S40
Row Sum
Percentage
input
25,392
27,378
25,425
27,851
23,145
23,565
24,941
23,728
24,749
31,000
19,731
21,438
28,106
26,831
24,793
29,330
20,896
16,722
26,285
21,821
30,575
33,770
36,605
39,287
39,557
37,580
35,732
39,788
29,892
34,942
49,462
29,049
23,810
29,634
35,042
35,354
22,399
26,652
25,191
24,171
1,151,619
100.00%
filtered
25,392
27,377
25,421
27,849
23,142
23,564
24,937
23,723
24,746
30,997
19,728
21,435
28,103
26,827
24,787
29,325
20,892
16,721
26,280
21,820
30,540
33,730
36,571
39,248
39,523
37,532
35,700
39,747
29,862
34,863
49,350
29,025
23,797
29,616
35,029
35,340
22,381
26,639
25,178
24,158
1,150,895
99.94%
denoisedF
23,896
26,168
24,458
26,424
21,893
22,369
23,671
22,324
23,419
29,638
18,437
20,419
26,912
25,426
23,556
28,204
19,461
15,626
24,932
20,330
29,357
32,756
35,466
37,816
38,309
35,894
33,885
38,195
28,756
33,110
47,992
27,464
21,821
28,428
33,560
33,135
21,224
25,523
23,860
22,820
1,096,934
95.25%
denoisedR
24,194
25,941
24,293
26,327
21,799
22,337
23,781
22,576
23,471
29,356
18,462
20,332
26,912
25,150
23,635
28,049
19,606
15,837
25,098
20,732
29,373
32,499
35,473
37,732
38,190
35,863
34,329
38,049
28,681
31,263
47,317
27,541
22,435
28,514
33,836
33,796
21,304
25,488
23,933
22,999
1,096,503
95.21%
merged
20,940
22,598
21,149
22,153
18,384
18,459
20,187
19,535
19,211
25,356
13,808
17,530
23,771
20,388
19,379
24,417
15,262
12,543
20,934
16,717
26,271
29,306
32,005
32,600
32,243
30,152
28,344
32,125
23,842
25,300
40,975
22,967
16,393
24,162
29,362
28,415
18,475
20,783
20,109
18,534
925,084
80.33%
nonchim
9,657
9,671
8,770
11,538
10,210
9,025
8,987
9,039
9,362
11,281
7,763
8,074
11,750
10,828
10,369
10,257
8,189
6,963
8,664
8,663
12,255
14,334
15,482
17,779
16,433
17,297
16,923
18,380
14,284
14,363
17,764
12,788
10,625
13,736
15,398
16,307
10,560
13,543
12,498
12,351
482,160
41.87%
This table can be downloaded as an Excel table below:
5. DADA2 Amplicon Sequence Variants (ASVs). A total of 6902 unique merged and chimera-free ASV sequences were identified, and their corresponding
read counts for each sample are available in the "ASV Read Count Table" with rows for the ASV sequences and columns for sample. This read count table can be used for
microbial profile comparison among different samples and the sequences provided in the table can be used to taxonomy assignment.
The species-level, open-reference 16S rRNA NGS reads taxonomy assignment pipeline
Version 20210310
1. Raw sequences reads in FASTA format were BLASTN-searched against a combined set of 16S rRNA reference sequences.
It consists of MOMD (version 0.1), the HOMD (version 15.2 http://www.homd.org/index.php?name=seqDownload&file&type=R ),
HOMD 16S rRNA RefSeq Extended Version 1.1 (EXT), GreenGene Gold (GG)
(http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/gold_strains_gg16S_aligned.fasta.gz) ,
and the NCBI 16S rRNA reference sequence set (https://ftp.ncbi.nlm.nih.gov/blast/db/16S_ribosomal_RNA.tar.gz).
These sequences were screened and combined to remove short sequences (<1000nt), chimera, duplicated and sub-sequences,
as well as sequences with poor taxonomy annotation (e.g., without species information).
This process resulted in 1,015 from HOMD V15.22, 495 from EXT, 3,940 from GG and 18,044 from NCBI, a total of 25,120 sequences.
Altogether these sequence represent a total of 15,601 oral and non-oral microbial species.
The NCBI BLASTN version 2.7.1+ (Zhang et al, 2000) was used with the default parameters.
Reads with ≥ 98% sequence identity to the matched reference and ≥ 90% alignment length
(i.e., ≥ 90% of the read length that was aligned to the reference and was used to calculate
the sequence percent identity) were classified based on the taxonomy of the reference sequence
with highest sequence identity. If a read matched with reference sequences representing
more than one species with equal percent identity and alignment length, it was subject
to chimera checking with USEARCH program version v8.1.1861 (Edgar 2010). Non-chimeric reads with multi-species
best hits were considered valid and were assigned with a unique species
notation (e.g., spp) denoting unresolvable multiple species.
2. Unassigned reads (i.e., reads with < 98% identity or < 90% alignment length) were pooled together and reads < 200 bases were
removed. The remaining reads were subject to the de novo
operational taxonomy unit (OTU) calling and chimera checking using the USEARCH program version v8.1.1861 (Edgar 2010).
The de novo OTU calling and chimera checking was done using 98% as the sequence identity cutoff, i.e., the species-level OTU.
The output of this step produced species-level de novo clustered OTUs with 98% identity.
Representative reads from each of the OTUs/species were then BLASTN-searched
against the same reference sequence set again to determine the closest species for
these potential novel species. These potential novel species were pooled together with the reads that were signed to specie-level in
the previous step, for down-stream analyses.
Reference:
Edgar RC. Search and clustering orders of magnitude faster than BLAST.
Bioinformatics. 2010 Oct 1;26(19):2460-1. doi: 10.1093/bioinformatics/btq461. Epub 2010 Aug 12. PubMed PMID: 20709691.
3. Designations used in the taxonomy:
1) Taxonomy levels are indicated by these prefixes:
k__: domain/kingdom
p__: phylum
c__: class
o__: order
f__: family
g__: genus
s__: species
Example:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__faecis
2) Unique level identified – known species:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__hominis
The above example shows some reads match to a single species (all levels are unique)
3) Non-unique level identified – known species:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__multispecies_spp123_3
The above example “s__multispecies_spp123_3” indicates certain reads equally match to 3 species of the
genus Roseburia; the “spp123” is a temporally assigned species ID.
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__multigenus;s__multispecies_spp234_5
The above example indicates certain reads match equally to 5 different species, which belong to multiple genera.;
the “spp234” is a temporally assigned species ID.
4) Unique level identified – unknown species, potential novel species:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ hominis_nov_97%
The above example indicates that some reads have no match to any of the reference sequences with
sequence identity ≥ 98% and percent coverage (alignment length) ≥ 98% as well. However this groups
of reads (actually the representative read from a de novo OTU) has 96% percent identity to
Roseburia hominis, thus this is a potential novel species, closest to Roseburia hominis.
(But they are not the same species).
5) Multiple level identified – unknown species, potential novel species:
k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ multispecies_sppn123_3_nov_96%
The above example indicates that some reads have no match to any of the reference sequences
with sequence identity ≥ 98% and percent coverage (alignment length) ≥ 98% as well.
However this groups of reads (actually the representative read from a de novo OTU)
has 96% percent identity equally to 3 species in Roseburia. Thus this is no single
closest species, instead this group of reads match equally to multiple species at 96%.
Since they have passed chimera check so they represent a novel species. “sppn123” is a
temporary ID for this potential novel species.
4. The taxonomy assignment algorithm is illustrated in this flow char below:
Read Taxonomy Assignment - Result Summary *
Code
Category
MPC=0% (>=1 read)
MPC=0.1%(>=481 reads)
A
Total reads
482,160
482,160
B
Total assigned reads
481,207
481,207
C
Assigned reads in species with read count < MPC
0
31,033
D
Assigned reads in samples with read count < 500
0
0
E
Total samples
40
40
F
Samples with reads >= 500
40
40
G
Samples with reads < 500
0
0
H
Total assigned reads used for analysis (B-C-D)
481,207
450,174
I
Reads assigned to single species
449,410
427,295
J
Reads assigned to multiple species
18,057
16,563
K
Reads assigned to novel species
13,740
6,316
L
Total number of species
409
133
M
Number of single species
266
122
N
Number of multi-species
19
5
O
Number of novel species
124
6
P
Total unassigned reads
953
953
Q
Chimeric reads
189
189
R
Reads without BLASTN hits
4
4
S
Others: short, low quality, singletons, etc.
760
760
A=B+P=C+D+H+Q+R+S
E=F+G
B=C+D+H
H=I+J+K
L=M+N+O
P=Q+R+S
* MPC = Minimal percent (of all assigned reads) read count per species, species with read count < MPC were removed.
* Samples with reads < 500 were removed from downstream analyses.
* The assignment result from MPC=0.1% was used in the downstream analyses.
Read Taxonomy Assignment - ASV Species-Level Read Counts Table
This table shows the read counts for each sample (columns) and each species identified based on the ASV sequences.
The downstream analyses were based on this table.
The species listed in the table has full taxonomy and a dynamically assigned species ID specific to this report.
When some reads match with the reference sequences of more than one species equally (i.e., same percent identiy and alignmnet coverage),
they can't be assigned to a particular species. Instead, they are assigned to multiple species with the species notaton
"s__multispecies_spp2_2". In this notation, spp2 is the dynamic ID assigned to these reads that hit multiple sequences and the "_2"
at the end of the notation means there are two species in the spp2.
You can look up which species are included in the multi-species assignment, in this table below:
Another type of notation is "s__multispecies_sppn2_2", in which the "n" in the sppn2 means it's a potential novel species because all the reads in this species
have < 98% idenity to any of the reference sequences. They were grouped together based on de novo OTU clustering at 98% identity cutoff. And then
a representative sequence was chosed to BLASTN search against the reference database to find the closest match (but will still be < 98%). This representative
sequence also matched equally to more than one species, hence the "spp" was given in the label.
In ecology, alpha diversity (α-diversity) is the mean species diversity in sites or habitats at a local scale.
The term was introduced by R. H. Whittaker[1][2] together with the terms beta diversity (β-diversity)
and gamma diversity (γ-diversity). Whittaker's idea was that the total species diversity in a landscape
(gamma diversity) is determined by two different things, the mean species diversity in sites or habitats
at a more local scale (alpha diversity) and the differentiation among those habitats (beta diversity).
Diversity measures are affected by the sampling depth. Rarefaction is a technique to assess species richness from the results of sampling. Rarefaction allows
the calculation of species richness for a given number of individual samples, based on the construction
of so-called rarefaction curves. This curve is a plot of the number of species as a function of the
number of samples. Rarefaction curves generally grow rapidly at first, as the most common species are found,
but the curves plateau as only the rarest species remain to be sampled.
The two main factors taken into account when measuring diversity are richness and evenness.
Richness is a measure of the number of different kinds of organisms present in a particular area.
Evenness compares the similarity of the population size of each of the species present. There are
many different ways to measure the richness and evenness. These measurements are called "estimators" or "indices".
Below is a diversity of 3 commonly used indices showing the values for all the samples (dots) and in groups (boxes).
Alpha Diversity Box Plots for All Groups
Alpha Diversity Box Plots for Individual Comparisons
To test whether the alpha diversity among different comparison groups are different statisticall, we use the Kruskal Wallis H test
provided the "alpha-group-significance" fucntion in the QIIME 2 diversity package. Kruskal Wallis H test is the non parametric alternative
to the One Way ANOVA. Non parametric means that the test doesn’t assume your data comes from a particular distribution. The H test is used
when the assumptions for ANOVA aren’t met (like the assumption of normality). It is sometimes called the one-way ANOVA on ranks,
as the ranks of the data values are used in the test rather than the actual data points. The test determines whether the medians of two
or more groups are different.
Below are the Kruskal Wallis H test results for each comparison based on three different alpha diversity measures: 1) Observed species (features),
2) Shannon index, and 3) Simpson index.
Beta diversity compares the similarity (or dissimilarity) of microbial profiles between different
groups of samples. There are many different similarity/dissimilarity metrics.
In general, they can be quantitative (using sequence abundance, e.g., Bray-Curtis or weighted UniFrac)
or binary (considering only presence-absence of sequences, e.g., binary Jaccard or unweighted UniFrac).
They can be even based on phylogeny (e.g., UniFrac metrics) or not (non-UniFrac metrics, such as Bray-Curtis, etc.).
For microbiome studies, species profiles of samples can be compared with the Bray-Curtis dissimilarity,
which is based on the count data type. The pair-wise Bray-Curtis dissimilarity matrix of all samples can then be
subject to either multi-dimensional scaling (MDS, also known as PCoA) or non-metric MDS (NMDS).
MDS/PCoA is a
scaling or ordination method that starts with a matrix of similarities or dissimilarities
between a set of samples and aims to produce a low-dimensional graphical plot of the data
in such a way that distances between points in the plot are close to original dissimilarities.
NMDS is similar to MDS, however it does not use the dissimilarities data, instead it converts them into
the ranks and use these ranks in the calculation.
In our beta diversity analysis, Bray-Curtis dissimilarity matrix was first calculated and then plotted by the PCoA and
NMDS separately. Below are beta diveristy results for all groups together:
NMDS and PCoA Plots for All Groups
The above PCoA and NMDS plots are based on count data. The count data can also be transformed into centered log ratio (CLR)
for each species. The CLR data is no longer count data and cannot be used in Bray-Curtis dissimilarity calculation. Instead
CLR can be compared with Euclidean distances. When CLR data are compared by Euclidean distance, the distance is also called
Aitchison distance.
Below are the NMDS and PCoA plots of the Aitchison distances of the samples:
Interactive 3D PCoA Plots - Bray-Curtis Dissimilarity
Interactive 3D PCoA Plots - Euclidean Distance
Interactive 3D PCoA Plots - Correlation Coefficients
Group Significance of Beta-diversity Indices
To test whether the between-group dissimilarities are significantly greater than the within-group dissimilarities,
the "beta-group-significance" function provided in the QIIME 2 "diversity" package was used with PERMANOVA
(permutational multivariate analysis of variance) chosen s the group significan testing method.
Three beta diversity matrics were used: 1) Bray–Curtis dissimilarity 2) Correlation coefficient matrix , and 3) Aitchison distance
(Euclidean distance between clr-transformed compositions).
16S rRNA next generation sequencing (NGS) generates a fixed number of reads that reflect the proportion of different
species in a sample, i.e., the relative abundance of species, instead of the absolute abundance.
In Mathematics, measurements involving probabilities, proportions, percentages, and ppm can all
be thought of as compositional data. This makes the microbiome read count data “compositional”
(Gloor et al, 2017). In general, compositional data represent parts of a whole which only
carry relative information (http://www.compositionaldata.com/).
The problem of microbiome data being compositional arises when comparing two groups of samples for
identifying “differentially abundant” species. A species with the same absolute abundance between two
conditions, its relative abundances in the two conditions (e.g., percent abundance) can become different
if the relative abundance of other species change greatly. This problem can lead to incorrect conclusion
in terms of differential abundance for microbial species in the samples.
When studying differential abundance (DA), the current better approach is to transform the read count
data into log ratio data. The ratios are calculated between read counts of all species in a sample to
a “reference” count (e.g., mean read count of the sample). The log ratio data allow the detection of DA
species without being affected by percentage bias mentioned above
In this report, a compositional DA analysis tool “ANCOM” (analysis of composition of microbiomes)
was used. ANCOM transforms the count data into log-ratios and thus is more suitable for comparing
the composition of microbiomes in two or more populations. "ANCOM" generates a table of features with
W-statistics and whether the null hypothesis is rejected. The “W” is the W-statistic, or number of
features that a single feature is tested to be significantly different against. Hence the higher the "W"
the more statistical sifgnificane that a feature/species is differentially abundant.
References:
Gloor GB, Macklaim JM, Pawlowsky-Glahn V, Egozcue JJ. Microbiome Datasets Are Compositional: And This Is Not Optional. Front Microbiol.
2017 Nov 15;8:2224. doi: 10.3389/fmicb.2017.02224. PMID: 29187837; PMCID: PMC5695134.
Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of
microbiomes: a novel method for studying microbial composition. Microb Ecol Health Dis.
2015 May 29;26:27663. doi: 10.3402/mehd.v26.27663. PMID: 26028277; PMCID: PMC4450248.
Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction.
Nat Commun. 2020 Jul 14;11(1):3514. doi: 10.1038/s41467-020-17041-7.
PMID: 32665548; PMCID: PMC7360769.
Starting with version V1.2, we also include the results of ANCOM-BC (Analysis of Compositions of
Microbiomes with Bias Correction) (Lin and Peddada 2020). ANCOM-BC is an updated version of "ANCOM" that:
(a) provides statistically valid test with appropriate p-values,
(b) provides confidence intervals for differential abundance of each taxon,
(c) controls the False Discovery Rate (FDR),
(d) maintains adequate power, and
(e) is computationally simple to implement.
The bias correction (BC) addresses a challenging problem of the bias introduced by differences in
the sampling fractions across samples. This bias has been a major hurdle in performing DA analysis of microbiome data.
ANCOM-BC estimates the unknown sampling fractions and corrects the bias induced by their differences among samples.
The absolute abundance data are modeled using a linear regression framework.
References:
Lin H, Peddada SD. Analysis of compositions of microbiomes with bias correction.
Nat Commun. 2020 Jul 14;11(1):3514. doi: 10.1038/s41467-020-17041-7.
PMID: 32665548; PMCID: PMC7360769.
LEfSe (Linear Discriminant Analysis Effect Size) is an alternative method to find "organisms, genes, or
pathways that consistently explain the differences between two or more microbial communities" (Segata et al., 2011).
Specifically, LEfSe uses rank-based Kruskal-Wallis (KW) sum-rank test to detect features with significant
differential (relative) abundance with respect to the class of interest. Since it is rank-based, instead of proportional based,
the differential species identified among the comparison groups is less biased (than percent abundance based).
Reference:
Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011 Jun 24;12(6):R60. doi: 10.1186/gb-2011-12-6-r60. PMID: 21702898; PMCID: PMC3218848.
To analyze the co-occurrence or co-exclusion between microbial species among different samples, network correlation
analysis tools are usually used for this purpose. However, microbiome count data are compositional. If count data are normalized to the total number of counts in the
sample, the data become not independent and traditional statistical metrics (e.g., correlation) for the detection
of specie-species relationships can lead to spurious results. In addition, sequencing-based studies typically
measure hundreds of OTUs (species) on few samples; thus, inference of OTU-OTU association networks is severely
under-powered. Here we use SPIEC-EASI (SParse InversECovariance Estimation
for Ecological Association Inference), a statistical method for the inference of microbial
ecological networks from amplicon sequencing datasets that addresses both of these issues (Kurtz et al., 2015).
SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model
inference framework that assumes the underlying ecological association network is sparse. SPIEC-EASI provides
two algorithms for network inferencing – 1) Meinshausen-Bühlmann's neighborhood selection (MB method) and inverse covariance selection
(GLASSO method, i.e., graphical least absolute shrinkage and selection operator). This is fundamentally distinct from SparCC, which essentially estimate pairwise correlations. In addition
to these two methods, we provide the results of a third method - SparCC (Sparse Correlations for Compositional Data)(Friedman & Alm 2012), which
is also a method for inferring correlations from compositional data. SparCC estimates the linear Pearson correlations between
the log-transformed components.
References:
Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA. Sparse and compositionally robust inference of microbial ecological networks. PLoS Comput Biol. 2015 May 7;11(5):e1004226. doi: 10.1371/journal.pcbi.1004226. PMID: 25950956; PMCID: PMC4423992.
